Nucleic acid detection using probes

ABSTRACT

The invention provides a method for detecting a target nucleotide sequence by tagging the nucleotide sequence with a nucleotide tag, providing a probe oligonucleotide with a melting temperature Tm1, comprising a regulatory sequence and a nucleotide tag recognition sequence; incorporating the probe oligonucleotide into the tagged polynucleotide in a polynucleotide amplification reaction, providing a regulatory oligonucleotide with a melting temperature Tm2, comprising a sequence segment that complementary to the regulatory sequence and a tail segment that does not hybridize to the probe nucleotide when the sequence segment and the regulatory sequence are annealed, amplifying the tagged target nucleic acid sequence in a PCR amplification reaction using the probe oligonucleotide as a primer, and using a DNA polymerase with high strand displacement activity and low 5′-nuclease activity, and detecting the amplification product; wherein Tm1 and Tm2 are higher than the annealing temperature associated with the polynucleotide amplification reaction.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a continuation of PCT/US2012/065376, filed Nov. 15,2012, and is a continuation-in-part of U.S. patent application Ser. No.14/340,446, filed Jul. 24, 2014, which is a continuation of U.S. patentapplication Ser. No. 13/467,933, filed May 9, 2012, now U.S. Pat. No.8,809,238 B2, issued Aug. 19, 2014, which claims the benefit of priorityof U.S. provisional application No. 61/484,198, filed May 9, 2011. Theentire contents of the above-referenced applications are incorporatedherein by reference.

REFERENCE TO A SEQUENCE LISTING

The Sequence Listing written in fileSequenceListing_85665-021710US-944685.txt, created on Aug. 26, 2015,14,982 bytes, machine format IBM-PC, MS-Windows operating system, ishereby incorporated by reference in its entirety for all purposes.

FIELD OF THE INVENTION

The invention relates to a PCR-based detection system suitable fornucleotide polymorphism (SNP) genotyping and other genetic assays.

BACKGROUND OF THE INVENTION

Fluorescent reporter molecule-quencher molecule pairs have beenincorporated onto probe oligonucleotides in order to monitor biologicalevents based on the fluorescent reporter molecule and quencher moleculebeing separated or brought within a minimum quenching distance of eachother. For example, probes have been developed where the intensity ofthe reporter molecule fluorescence increases due to the separation ofthe reporter molecule from the quencher molecule. Probes have also beendeveloped which lose their fluorescence because the quencher molecule isbrought into proximity with the reporter molecule. Thesereporter-quencher molecule pair probes have been used to monitorhybridization assays and nucleic acid amplification reactions,especially polymerase chain reactions (PCR), by monitoring either theappearance or disappearance of the fluorescence signal generated by thereporter molecule.

One particularly important application for probes including areporter-quencher molecule pair is their use in nucleic acidamplification reactions, such as polymerase chain reactions (PCR), todetect the presence and amplification of a target nucleic acid sequence.In general, nucleic acid amplification techniques have opened broad newapproaches to genetic testing and DNA analysis. Arnheim and Erlich, Ann.Rev. Biochem., 61: 131-156 (1992). PCR, in particular, has become aresearch tool of major importance with applications in, for example,cloning, analysis of genetic expression, DNA sequencing, genetic mappingand drug discovery. Arnheim and Erlich, Ann. Rev. Biochem., 61: 131-156(1992); Gilliland et al., Proc. Natl. Acad. Sci., 87: 2725-2729 (1990);Bevan et al., PCR Methods and Applications, 1: 222-228 (1992); Green etal., PCR Methods and Applications, 1:77-90 (1991); Blackwell et al.,Science, 250: 1104-1110 (1990).

SUMMARY OF THE INVENTION

In one aspect, the invention provides a method for detecting a targetpolynucleotide sequence in a sample, comprising a) combining i) a probeoligonucleotide that hybridizes to the target polynucleotide and acts asa forward primer for PCR amplification, comprising a nucleotide tagrecognition sequence, a regulatory sequence positioned 5′ to thenucleotide tag recognition sequence, and a reporter moiety; ii) a primerthat hybridizes to the target polynucleotide and acts as a reverseprimer for PCR amplification; iii) a thermostable DNA polymerase, b)amplifying the target polynucleotide sequence in a PCR amplificationreaction using said probe oligonucleotide and said primer, therebyproducing an amplicon comprising the regulatory sequence; wherein thePCR amplification reaction is carried out in the presence of aregulatory oligonucleotide comprising i) a sequence segment that iscomplementary to the regulatory sequence, ii) a 5′ tail segment that isnot complementary to the probe oligonucleotide; and iii) a quenchermoiety wherein the reporter moiety and the quencher moiety arefluorescent reporter-quencher pair; wherein the sequence segment of theregulatory oligonucleotide hybridizes to said regulatory sequence in onestrand of said amplicon, whereby the signal from the reporter moiety isquenched by quenching moiety; and c) detecting a signal produced by thefluorescent reporter, said signal resulting from the displacement of theregulatory oligonucleotide from the amplicon.

In an embodiment the probe oligonucleotide has a melting temperatureTm1, regulatory oligonucleotide has a melting temperature Tm2; the PCRamplification reaction is characterized by an annealing temperature Ta;and Tm1 and Tm2 are both higher than Ta.

In a related aspect the invention provides a method for detecting atarget nucleotide sequence comprising: a) tagging the target nucleotidesequence with a nucleotide tag sequence, thereby producing a taggedtarget nucleic acid sequence; b) providing a probe oligonucleotidecomprising a nucleotide tag recognition sequence complementary to thenucleotide tag sequence and a regulatory sequence 5′ to the nucleotidetag recognition sequence, wherein said probe oligonucleotide comprises afirst label and has a melting temperature Tm1; c) amplifying the taggedtarget nucleic acid sequence in a PCR amplification reaction using theprobe oligonucleotide as a primer, wherein said PCR amplificationreaction is characterized by an annealing temperature Ta; wherein thePCR amplification reaction is carried out in the presence of aregulatory oligonucleotide comprising a sequence segment that iscomplementary to the regulatory sequence and a tail segment with asequence not complementary to the probe oligonucleotide sequence,wherein said regulatory oligonucleotide comprises a second label and hasa melting temperature Tm2; and d) detecting the product of the PCRamplification reaction; wherein the first label and the second labelconstitute a fluorescent reporter/quencher pair; and wherein Tm1 and Tm2are both higher than Ta.

In some embodiments the thermostable DNA polymerase has standdisplacement activity that is greater than the strand displacementactivity of native Thermus aquaticus (Taq) DNA polymerase. In someembodiments the thermostable DNA polymerase has stand displacementactivity that is at least as great as the displacement activity ofThermococcus litoralis DNA polymerase. In some embodiments thethermostable DNA polymerase has 5′-exonuclease activity that is lowerthan that of not higher than that of native Thermus aquaticus (Taq) DNApolymerase. In some embodiments the thermostable DNA polymerase has5′-exonuclease activity that is not higher than that of Thermococcuslitoralis DNA polymerase. In some embodiments the thermostable DNApolymerase is a recombinant DNA polymerase derived from a naturallyoccurring thermostable DNA polymerase, wherein the thermostable DNApolymerase has reduced 5′ nuclease activity compared to the naturallyoccurring DNA polymerase. In some embodiments the thermostable DNApolymerase is a recombinant DNA polymerase derived from Thermusaquaticus (Taq) DNA polymerase. In some embodiments the thermostable DNApolymerase is Thermococcus litoralis DNA polymerase, Bacillusstearothermophilus DNA polymerase or Bacillus caldotenax DNA polymerase,or a recombinant DNA polymerase derived from Thermococcus litoralis DNApolymerase, Bacillus stearothermophilus DNA polymerase or Bacilluscaldotenax DNA polymerase. In some embodiments the nucleotide tagsequence is incorporated into the tagged target nucleic acid sequenceusing a PCR reaction. In some embodiments the nucleotide tag recognitionsequence is exactly complementary to the nucleotide tag sequence. Insome embodiments the regulatory oligonucleotide comprises a sequencesegment that is exactly complementary to regulatory sequence. In someembodiments the regulatory oligonucleotide has a length in the range of15-45 nucleotides. In some embodiments the Ta is in the range of 55-64°C. In some embodiments the PCR amplification reaction comprises at least20 cycles at the annealing temperature (Ta). In some embodiments thetail segment of the regulatory oligonucleotide has a length of from 5 toabout 25 bases, such as a length of 5-8 bases. In some embodiments thetail segment is at least about 70% GC. In some embodiments the tailsegment is 100% noncomplementary to the region of the probeoligonucleotide to which it corresponds when the regulatoryoligonucleotide is aligned to the probe nucleotide.

In one aspect, the invention provides a method for detecting a targetnucleotide sequence comprising:

a) tagging the target nucleotide sequence with a nucleotide tagsequence, thereby producing a tagged target nucleic acid sequence;

b) providing a probe oligonucleotide comprising a nucleotide tagrecognition sequence complementary to the nucleotide tag sequence and aregulatory sequence 5′ to the nucleotide tag recognition sequence,wherein said probe oligonucleotide comprises a first label and has amelting temperature Tm1;

c) amplifying the tagged target nucleic acid sequence in a PCRamplification reaction using the probe oligonucleotide as a primer,wherein said PCR amplification reaction is characterized by an annealingtemperature Ta;

wherein the PCR amplification reaction is carried out in the presence ofa regulatory oligonucleotide comprising a sequence segment that iscomplementary to the regulatory sequence and a tail segment with asequence not complementary to the probe oligonucleotide sequence,wherein said regulatory oligonucleotide comprises a second label and hasa melting temperature T_(M)2; and

d) detecting the product of the PCR amplification reaction;

wherein the first label and the second label constitute a fluorescentreporter/quencher pair; and wherein T_(M)1 and T_(M)2 are both higherthan Ta.

In an embodiment, the tag sequence is incorporated into the taggedtarget nucleic acid sequence using a PCR reaction.

In an embodiment, the nucleotide tag recognition sequence is exactlycomplementary to the nucleotide tag sequence. In an embodiment, theregulatory oligonucleotide comprises a sequence segment that is exactlycomplementary to regulatory sequence. In an embodiment, the regulatoryoligonucleotide has a length in the range of 15-45 nucleotides. In anembodiment, Ta is in the range of 55-62° C. In an embodiment, Ta is inthe range of 60-64° C. In an embodiment, Ta is in the range of 60°C.-62° C. In some embodiments, Tm1 is at least 25° C. higher than theannealing temperature (Ta). In some embodiments, Tm2 is at least atleast 2° C., at least 3° C., at least 4° C., at least 5° C., or at least10° C. higher than the annealing temperature (Ta). In some embodimentsTm2 is in the range of 60-75° C. In some embodiments, Tm1 and Tm2 arecalculated by the formula: T_(m) (° C.)=4(G+C)+2(A+T).

In some embodiments the PCR amplification reaction is carried out in areaction volume greater than 500 nL, or greater than 1 uL. For example,in some embodiments the PCR amplification reactions are carried out in amultiwell plate comprising 96-1536 wells. In some embodiments, Ta isabout 57° C.

In some embodiments the PCR amplification reaction is carried out in areaction volume less than 100 nL. In some embodiments the PCRamplification reaction is carried out in a microfluidic device. In someembodiments Ta is about 60° C.

In certain embodiments, Ta is the yielding annealing temperature. Insome embodiments the PCR amplification reaction comprises at least 20cycles at the annealing temperature (Ta).

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 illustrates an assay for genotyping. T=target sequence, orcomplement; X, Y=tag sequence, or complement, R_(G), R_(R)=reporters,Q=quencher(s), z, w=regulatory sequence, or complement, “L1” and“L2”=independently selected tail (unhybridized) segments, or complement.

FIGS. 2A-B contrast the present invention (A) in which a “tailed”regulatory oligonucleotide is used and (B) the same assay in which theregulatory oligonucleotide is not tailed. As shown in FIG. 2A, anallele-specific primer possessing a universal coding sequence and areverse primer participate in a PCR reaction to generate an encodedamplicon. A probe oligonucleotide comprising a fluorescent reportermoiety and further comprising a region complementary to the encodedregion of the amplicon, and a regulatory oligonucleotide with a segmentthat is complementary to a portion of the probe oligonucleotide andfurther comprises an noncomplementary (tail) region, are present in thereaction mixture. The fluorescently labeled probe oligonucleotide actsas a forward primer in a subsequent PCR reaction step and isincorporated into a new amplicon. The regulatory oligonucleotidehybridizes to the incorporated probe oligonucleotide sequence, quenchingthe reporter signal. The regulatory oligonucleotide is displaced by theaction of a polymerase with high strand displacement activity and low 5′nuclease activity, resulting in the fluorescence from the (unquenched)reporter. Preservation of the integrity of the regulatoryoligonucleotide is advantageous so that it remains available tohybridize and quench fluorescence from nonincorporated probeoligonucleotide in the reaction mixture. The displaced, but intact,regulatory oligonucleotide binds free probe oligonucleotide, decreasingbackground fluorescence. In contrast, as illustrated in FIG. 2B, theomission of the noncomplementary sequence (“tail”) from the regulatoryoligonucleotide can result in digestion of the regulatoryoligonucleotide. Thermostable DNA polymerases are represented by acircle and arrows.

DETAILED DESCRIPTION A. Definitions

Terms used in the claims and specification are defined as set forthbelow unless otherwise specified. These terms are defined specificallyfor clarity, but all of the definitions are consistent with how askilled person in the art would understand these terms.

It also noted that as used herein and in the appended claims, thesingular forms “a,” “an,” and “the” include the plural reference unlessthe context clearly dictates otherwise. Thus, for example, a referenceto “a cell” is a reference to one or more cells and equivalents thereofknown to those skilled in the art.

As used herein, “immobilized” means insolubilized or comprising,attached to or operatively associated with an insoluble, partiallyinsoluble, colloidal, particulate, dispersed, suspended and/ordehydrated substance or a molecule or solid phase comprising or attachedto a solid support.

As used herein, “solid support” refers to a composition comprising animmobilization matrix such as but not limited to, insolubilizedsubstance, solid phase, surface, substrate, layer, coating, woven ornonwoven fiber, matrix, crystal, membrane, insoluble polymer, plastic,glass, biological or biocompatible or bioerodible or biodegradablepolymer or matrix, microparticle or nanoparticle. Solid supportsinclude, for example and without limitation, monolayers, bilayers,commercial membranes, resins, matrices, fibers, separation media,chromatography supports, polymers, plastics, glass, mica, gold, beads,microspheres, nanospheres, silicon, gallium arsenide, organic andinorganic metals, semiconductors, insulators, microstructures andnanostructures. Microstructures and nanostructures may include, withoutlimitation, microminiaturized, nanometer-scale and supramolecularprobes, tips, bars, pegs, plugs, rods, sleeves, wires, filaments, andtubes.

The term “adjacent,” when used herein to refer two nucleotide sequencesin a nucleic acid, can refer to nucleotide sequences separated by 0(zero) to about 20 nucleotides, more specifically, separated by about 1to about 10 nucleotides, or sequences that directly abut one another(i.e., separated by zero nucleotides).

The term “nucleic acid” refers to a nucleotide polymer, and unlessotherwise limited, includes analogs of natural nucleotides that canfunction in a similar manner (e.g., hybridize) to naturally occurringnucleotides. Unless otherwise limited “nucleic acids” can include, inaddition to the standard bases adenine, cytosine, guanine, thymine anduracil, various naturally occurring and synthetic bases (e.g., inosine),nucleotides and/or backbones.

The term nucleic acid includes any form of DNA or RNA, including, forexample, genomic DNA; complementary DNA (cDNA), which is a DNArepresentation of mRNA, usually obtained by reverse transcription ofmessenger RNA (mRNA) or by amplification; DNA molecules producedsynthetically or by amplification; and mRNA.

The term nucleic acid encompasses double- or triple-stranded nucleicacids, as well as single-stranded molecules. In double- ortriple-stranded nucleic acids, the nucleic acid strands need not becoextensive (i.e., a double-stranded nucleic acid need not bedouble-stranded along the entire length of both strands).

The term nucleic acid also encompasses any chemical modificationthereof, such as by methylation and/or by capping. Nucleic acidmodifications can include addition of chemical groups that incorporateadditional charge, hydrogen bonding, electrostatic interaction, andfunctionality to the individual nucleic acid bases or to the nucleicacid as a whole. Such modifications may include base modifications suchas 2-position sugar modifications, 5-position pyrimidine modifications,8-position purine modifications, modifications at cytosine exocyclicamines, substitutions of 5-bromo-uracil, backbone modifications, unusualbase pairing combinations such as the isobases isocytidine andisoguanidine, and the like.

More particularly, in certain embodiments, nucleic acids, can includepolydeoxyribonucleotides (containing 2-deoxy-D-ribose),polyribonucleotides (containing D-ribose), and any other type of nucleicacid that is an N- or C-glycoside of a purine or pyrimidine base, aswell as other polymers containing normucleotidic backbones, for example,polyamide (e.g., peptide nucleic acids (PNAs)) and polymorpholino(commercially available from the Anti-Virals, Inc., Corvallis, Oreg., asNeugene) polymers, and other synthetic sequence-specific nucleic acidpolymers providing that the polymers contain nucleobases in aconfiguration which allows for base pairing and base stacking, such asis found in DNA and RNA. The term nucleic acid also encompasses linkednucleic acids (LNAs), which are described in U.S. Pat. Nos. 6,794,499,6,670,461, 6,262,490, and 6,770,748, each of which is incorporatedherein by reference.

The nucleic acid(s) can be derived from a completely chemical synthesisprocess, such as a solid phase-mediated chemical synthesis, from abiological source, such as through isolation from any species thatproduces nucleic acid, or from processes that involve the manipulationof nucleic acids by molecular biology tools, such as DNA replication,PCR amplification, reverse transcription, or from a combination of thoseprocesses.

The term “target nucleic acids” is used herein to refer to particularnucleic acids to be detected in the methods of the invention.

As used herein the term “target nucleotide sequence” refers to anucleotide sequence of interest, such as, for example, the amplificationproduct obtained by amplifying a target nucleic acid or the cDNAproduced upon reverse transcription of an RNA target nucleic acid. Inthe case of RNA, the target nucleotide sequence can substitute thymidine(T) for uracil (U).

As used herein, the term “complementary” refers to the capacity forprecise pairing between two nucleotides. I.e., if a nucleotide at agiven position of a nucleic acid is capable of hydrogen bonding with anucleotide of another nucleic acid, then the two nucleic acids areconsidered to be complementary to one another at that position. A“complement” may be an exactly or partially complementary sequence.Complementarity between two single-stranded nucleic acid molecules maybe “partial,” in which only some of the nucleotides bind, or it may becomplete when total complementarity exists between the single-strandedmolecules. Two oligonucleotides are considered to have “complementary”sequences when there is sufficient complementarity that the sequenceshybridize (forming a double stranded region) under assay conditions. Thedegree of complementarity between nucleic acid strands has significanteffects on the efficiency and strength of hybridization between nucleicacid strands. Two sequences that are partially complementary may have,for example, at least 90% identity, or at least 95%, 96%, 97%, 98%, or99% identity sequence over a sequence of at least 7 nucleotides, moretypically over a sequence of 10-30 nucleotides, often over a sequence of14-25 nucleotides, and sometimes over a longer sequence (e.g., 26-100nucleotides in length). It will be understood that the 3′ base of aprimer sequence will desirably be perfectly complementary tocorresponding bases of the target nucleic acid sequence to allow primingto occur.

“Specific hybridization” refers to the binding of a nucleic acid to atarget nucleotide sequence in the absence of substantial binding toother nucleotide sequences present in the hybridization mixture underdefined stringency conditions. Those of skill in the art recognize thatrelaxing the stringency of the hybridization conditions allows sequencemismatches to be tolerated. In particular embodiments, hybridizationsare carried out under stringent hybridization conditions.

“T_(M)” refers to “melting temperature”, which is the temperature atwhich a population of double-stranded nucleic acid molecules becomeshalf-dissociated into single strands. The T_(M) of a single strandedoligonucleotide, as used herein, refers to the T_(M) of a doublestranded molecule comprising the oligonucleotide and its exactcomplement. Reporters or quenchers are not included in the determinationof T_(M). As used herein, T_(M) may be determined by calculation.Specifically, the T_(m) of an oligonucleotide may be a calculated T_(m)according to the equation: “T_(M) (° C.)=4(G+C)+2(A+T)” (Thein andWallace, 1986, in Human Genetic Disorders, p 33-50, IRL Press, OxfordUK, incorporated herein by reference). Other methods may be used todetermine melting temperature, both by calculation and empirically. SeeSantaLucia, J., Jr. “Physical Principles and Visual-OMP Software forOptimal PCR Design”, Methods in Molecular Biology: PCR Primer Design,Anton Yuryev, Ed., Humana Press, Totowa, N.J., Methods Mol. Biol. 402,3-34 (2007). Burpo, 2001, “A critical review of PCR primer designalgorithms and cross-hybridization case study” Biochemistry 281:1-11;Rychlik et al., 1990, “Optimization of the annealing temperature for DNAamplification in vitro” Nuc. Acid. Res. 18:6409-11; SantaLucia, 1998, “Aunified view of polymer, dumbbell, and oligonucleotide DNAnearest-neighbor thermodynamics” PNAS 95:41460-65; Lowe et al., 1990, “Acomputer program for selection of oligonucleotide primers for polymerasechain reactions” Nucleic Acids Res. 18:1757-61. Sambrook et al.,MOLECULAR CLONING: A LABORATORY MANUAL (C.S.H.P. Press, NY 2d ed., 1989)provides the Bolton and McCarthy calculation which corrects for thelength of the oligonucleotide. Also see Ausubel et al., CURRENTPROTOCOLS IN MOLECULAR BIOLOGY, Greene Publishing and WileyInterscience, New York (1997). Each of the aforementioned references isincorporated herein by reference in its entirety and particular for itsteaching of T_(M).

The term “oligonucleotide” is used to refer to a nucleic acid that isrelatively short, generally shorter than 200 nucleotides, moreparticularly, shorter than 100 nucleotides, most particularly, shorterthan 50 nucleotides. Typically, oligonucleotides are single-stranded DNAmolecules. Oligonucleotides used in the invention can be chemicallymodified. Chemical modifications can equip the oligonucleotides withadditional functionalities, such as chemical activity, affinity orprotection from degradations, e.g. by nucleases.

The term “primer” refers to an oligonucleotide that is capable ofhybridizing (also termed “annealing”) with a nucleic acid and serving asan initiation site for nucleotide (RNA or DNA) polymerization underappropriate conditions (e.g., in the presence of four differentnucleoside triphosphates and an agent for polymerization, such as DNA orRNA polymerase or reverse transcriptase) in an appropriate buffer and ata suitable temperature. The appropriate length of a primer depends onthe intended use of the primer, but primers are typically at least 7nucleotides long and, more typically range from 10 to 30 nucleotides, oreven more typically from 15 to 30 nucleotides, in length. Other primerscan be somewhat longer, e.g., 30 to 60 nucleotides long. In thiscontext, “primer length” refers to the portion of an oligonucleotide ornucleic acid that hybridizes to a complementary “target” sequence andprimes nucleotide synthesis. Short primer molecules generally requirecooler temperatures to form sufficiently stable hybrid complexes withthe template. A primer need not reflect the exact sequence of thetemplate but must be sufficiently complementary to hybridize with atemplate. The term “primer site” or “primer binding site” refers to thesegment of the target nucleic acid to which a primer hybridizes.

A primer is said to anneal to another nucleic acid if the primer, or aportion thereof, hybridizes to a nucleotide sequence within the nucleicacid. The statement that a primer hybridizes to a particular nucleotidesequence is not intended to imply that the primer hybridizes eithercompletely or exclusively to that nucleotide sequence. For example, incertain embodiments, amplification primers used herein are said to“anneal to a nucleotide tag”. This description encompasses probe/primersthat anneal wholly to the nucleotide tag, as well as probe/primers thatanneal partially to the nucleotide tag and partially to an adjacentnucleotide sequence, e.g., a target nucleotide sequence. Such hybridprimers can increase the specificity of the amplification reaction.

As used herein, the selection of primers “so as to avoid substantialannealing to the target nucleic acids” means that primers are selectedso that the majority of the amplicons detected after amplification are“full-length” in the sense that they result from priming at the expectedsites at each end of the target nucleic acid, as opposed to ampliconsresulting from priming within the target nucleic acid, which producesshorter-than-expected amplicons. In various embodiments, primers areselected so that at least 55%, at least 60%, at least 65%, at least 70%,at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, atleast 96%, at least 97%, at least 98%, or at least 99% of amplicons arefull-length.

The term “primer pair” refers to a set of primers including a 5′“upstream primer” or “forward primer” that hybridizes with thecomplement of the 5′ end of the DNA sequence to be amplified and a 3′“downstream primer” or “reverse primer” that hybridizes with the 3′ endof the sequence to be amplified. As will be recognized by those of skillin the art, the terms “upstream” and “downstream” or “forward” and“reverse” are not intended to be limiting, but rather provideillustrative orientation in particular embodiments.

A “probe” is a nucleic acid capable of binding to a target nucleic acidof complementary sequence through one or more types of chemical bonds,generally through complementary base pairing, usually through hydrogenbond formation, thus forming a duplex structure. The probe binds orhybridizes to a “probe binding site.” The probe can be labeled with adetectable label to permit facile detection of the probe, particularlyonce the probe has hybridized to its complementary target.Alternatively, however, the probe may be unlabeled, but may bedetectable by specific binding with a ligand that is labeled, eitherdirectly or indirectly. Probes can vary significantly in size.Generally, probes are at least 7 to 15 nucleotides in length. Otherprobes are at least 20, 30, or 40 nucleotides long. Still other probesare somewhat longer, being at least 50, 60, 70, 80, or 90 nucleotideslong. Yet other probes are longer still, and are at least 100, 150, 200or more nucleotides long. Probes can also be of any length that iswithin any range bounded by any of the above values (e.g., 15-20nucleotides in length).

A primer or probe sequence can be perfectly complementary to thesequence to which it hybridizes or can be less than perfectlycomplementary. In certain embodiments, the primer or probe sequence hasat least 65% identity to the complement of the target nucleic acidsequence over a sequence of at least 7 nucleotides, more typically overa sequence in the range of 10-30 nucleotides, and often over a sequenceof at least 14-25 nucleotides, and more often has at least 75% identity,at least 85% identity, at least 90% identity, or at least 95%, 96%, 97%.98%, or 99% identity. It will be understood that certain bases (e.g.,the 3′ base of a primer) are generally desirably perfectly complementaryto corresponding bases of the target nucleic acid sequence.

The terms “nucleotide tag sequence,” “nucleotide tag” and “tag sequence”are used herein to refer to a predetermined nucleotide sequence that isadded to a target nucleotide sequence. The nucleotide tag can encodeinformation about the target nucleotide sequence, such the identity ofthe target nucleotide sequence or the identity of the sample from whichthe target nucleotide sequence was derived. In certain embodiments, suchinformation may be encoded in one or more nucleotide tags, e.g., acombination of two nucleotide tags, one on either end of a targetnucleotide sequence, can encode the identity of the target nucleotidesequence.

As used herein, the term “encoding reaction” refers to reaction in whichat least one nucleotide tag is added to a target nucleotide sequence.This process may be referred to as “tagging.” Nucleotide tags can beadded, for example, by an “encoding PCR” in which the at least oneprimer comprises a target-specific portion and a nucleotide tag locatedon the 5′ end of the target-specific portion, and a second primer thatcomprises only a target-specific portion or a target-specific portionand a nucleotide tag located on the 5′ end of the target-specificportion. For illustrative examples of PCR protocols applicable toencoding PCR, see, e.g., PCT Publication Nos. WO 2004/051218 and WOUS03/37808, as well as U.S. Pat. No. 6,605,451, which are herebyincorporated by reference in their entirety. Nucleotide tags can also beadded by an “encoding ligation” reaction that can comprise a ligationreaction in which at least one primer comprises a target-specificportion and nucleotide tag located on the 5′ end of the target-specificportion, and a second primer that comprises a target-specific portiononly or a target-specific portion and a nucleotide tag located on the 5′end of the target specific portion. Illustrative encoding ligationreactions are described, for example, in U.S. Pat. No. 7,601,821 andPatent Publication No. 2005/0260640, which is hereby incorporated byreference in its entirety, and in particular for ligation reactions.Nucleotide tags can also be added by other amplification methods; seebelow.

As used herein an “encoding reaction” produces a “tagged targetnucleotide sequence” or “tagged target polynucleotide”, which include anucleotide tag linked to a target nucleotide sequence.

As used herein with reference to a portion of a primer, the term“target-specific” nucleotide sequence refers to a sequence that canspecifically anneal to a target nucleic acid or a target nucleotidesequence under suitable annealing conditions.

As used herein with reference to a portion of a probe/primer, the term“nucleotide tag recognition sequence” refers to a sequence that canspecifically anneal to a nucleotide tag under suitable annealingconditions.

“Amplification,” according to the present teachings encompasses anymeans by which at least a part of at least one target nucleic acid isreproduced, typically in a template-dependent manner, including withoutlimitation, a broad range of techniques for amplifying nucleic acidsequences, either linearly or exponentially. In general, practice of thepresent invention involves amplification using the polymerase chainreaction (PCR) and its well-known variants. PCR is an amplificationmethod in which thermal cycling, consisting of cycles of repeatedheating and cooling of the reaction for DNA melting and enzymaticreplication of the DNA. PCR Thermal cycling protocols are well known inthe art. Typically, PCR consists of a series of 20-40 cycles but feweror more cycles may be used in particular applications. For example, andnot limitation the cycle may include a denaturation step, an annealingstep (allowing annealing of the primers to the single-stranded DNAtemplate) and an extension/elongation step. Each step may occur at aparticular temperature, for a particular length of time, and underparticular reaction conditions. For example, and not for limitation, thetemperature of the denaturation step may be 95° C., the temperature ofthe annealing step (Ta) may be 62° C., and the temperature of theextension/elongation step may be 72° C. In some PCR protocols (e.g.,touchdown PCR) a high annealing temperature in initial cycles may bedecreased in increments in later cycles (reviewed in Korbie and Mattick,2008, “Touchdown PCR for increased specificity and sensitivity in PCRamplification” Nat Protoc. 3:1452-6). For purposes of the invention, insuch protocols, the Ta is defined as the annealing temperature used inthe majority of the cycles. Descriptions of PCR can be found in, amongother sources, Ausbel et al.; PCR Primer: A Laboratory Manual,Diffenbach, Ed., Cold Spring Harbor Press (1995); The ElectronicProtocol Book, Chang Bioscience (2002); Msuih et al., J. Clin. Micro.34:501-07 (1996); The Nucleic Acid Protocols Handbook, R. Rapley, ed.,Humana Press, Totowa, N.J. (2002); Abramson et al., Curr OpinBiotechnol. 1993 February; 4(1):41-7.

The term “qPCR” is used herein to refer to quantitative real-timepolymerase chain reaction (PCR), which is also known as “real-time FOR”or “kinetic polymerase chain reaction.”

A “reagent” refers broadly to any agent used in a reaction, other thanthe analyte (e.g., nucleic acid being analyzed). Illustrative reagentsfor a nucleic acid amplification reaction include, but are not limitedto, buffer, metal ions, polymerase, reverse transcriptase, primers,template nucleic acid, nucleotides, labels, dyes, nucleases, and thelike. Reagents for enzyme reactions include, for example, substrates,cofactors, buffer, metal ions, inhibitors, and activators.

The term “label,” as used herein, refers to any atom or molecule thatcan be used to provide a detectable and/or quantifiable signal. Inparticular, the label can be attached, directly or indirectly, to anucleic acid or protein. Suitable labels that can be attached to probesinclude, but are not limited to, radioisotopes, fluorophores,chromophores, mass labels, electron dense particles, magnetic particles,spin labels, molecules that emit chemiluminescence, electrochemicallyactive molecules, enzymes, cofactors, and enzyme substrates.

The term “dye,” has its standard meaning in the art. The term“fluorescent dye,” as used herein, generally refers to any dye thatemits electromagnetic radiation of longer wavelength by a fluorescentmechanism upon irradiation by a source of electromagnetic radiation,such as a lamp, a photodiode, or a laser.

The term “reporter molecule” refers to a molecule capable of generatinga fluorescence signal. A “quencher molecule” refers to a moleculecapable of absorbing the fluorescence energy of an excited reportermolecule, thereby quenching the fluorescence signal that would otherwisebe released from the excited reporter molecule. In order for a quenchermolecule to quench an excited fluorophore, it is often advantageous thatthe quencher molecule is within a minimum quenching distance of theexcited reporter molecule at some time starting from the excitation ofthe reporter molecule, but prior to the reporter molecule releasing thestored fluorescence energy. In proximity based quenching applications,the reporter and quencher molecules are positioned sufficiently close toeach other such that whenever the reporter molecule is excited, theenergy of the excited state transfers to the quencher molecule where iteither dissipates nonradiatively or is emitted at a different emissionfrequency than that of the reporter molecule. Several non-radiativeenergy transfer mechanisms work over shorter distances and areappropriate for proximity based quenching applications.

A “polymorphic marker” or “polymorphic site” is a locus at which anucleotide sequence divergence occurs. Illustrative markers have atleast two alleles, each typically occurring at a frequency of greaterthan 1%, and more typically greater than 10% or 20% of a selectedpopulation. A polymorphic site may be as small as one base pair.Polymorphic markers include restriction fragment length polymorphism(RFLPs), variable number of tandem repeats (VNTR's), hypervariableregions, minisatellites, dinucleotide repeats, trinucleotide repeats,tetranucleotide repeats, simple sequence repeats, deletions, andinsertion elements such as Alu. The first identified allelic form isarbitrarily designated as the reference form and other allelic forms aredesignated as alternative or variant alleles. The allelic form occurringmost frequently in a selected population is sometimes referred to as thewildtype form. Diploid organisms may be homozygous or heterozygous forallelic forms. A diallelic polymorphism has two forms. A triallelicpolymorphism has three forms.

A “single nucleotide polymorphism” (SNP) occurs at a polymorphic siteoccupied by a single nucleotide, which is the site of variation betweenallelic sequences. The site is usually preceded by and followed byhighly conserved sequences of the allele (e.g., sequences that vary inless than 1/100 or 1/1000 members of the populations). A SNP usuallyarises due to substitution of one nucleotide for another at thepolymorphic site. A transition is the replacement of one purine byanother purine or one pyrimidine by another pyrimidine. A transversionis the replacement of a purine by a pyrimidine or vice versa. SNPs canalso arise from a deletion of a nucleotide or an insertion of anucleotide relative to a reference allele.

B. Description

In one aspect, the invention provides a method for detecting a targetnucleotide sequence comprising: a) tagging the target nucleotidesequence with a nucleotide tag sequence, thereby producing a taggedtarget nucleic acid sequence; b) providing a probe oligonucleotidecomprising a nucleotide tag recognition sequence complementary to thenucleotide tag sequence and a regulatory sequence 5′ to the nucleotidetag recognition sequence, wherein said probe oligonucleotide comprises afirst label and has a melting temperature T_(M)1; c) amplifying thetagged target nucleic acid sequence in a PCR amplification reactionusing the probe oligonucleotide as a primer, wherein said PCRamplification reaction is characterized by an annealing temperature Ta;wherein the PCR amplification reaction is carried out in the presence ofa regulatory oligonucleotide comprising a sequence segment that iscomplementary to the regulatory sequence, wherein said regulatoryoligonucleotide comprises a second label and has a melting temperatureT_(M)2; and d) detecting the product of the PCR amplification reaction;wherein the first label and the second label constitute a fluorescentreporter/quencher pair; and wherein Tm1 and T_(M)2 are both higher thanTa. Without intending to be bound by a particular mechanism, carryingout a reaction in which both the Tm of the probe oligonucleotide and theT_(M) regulatory oligonucleotide are above Ta, reduces background signal(fluorescence) and provides a superior assay result.

In one aspect, the invention provides a method for detecting apolynucleotide with a target nucleotide sequence by tagging thepolynucleotide comprising a desired target nucleotide sequence with anucleotide tag, providing a probe oligonucleotide with a meltingtemperature Tm1, comprising a regulatory sequence and a nucleotide tagrecognition sequence; incorporating the probe oligonucleotide sequenceinto the tagged polynucleotide in a polynucleotide amplificationreaction, providing a regulatory oligonucleotide with a meltingtemperature Tm2, comprising a sequence segment that is at leastpartially complementary to the regulatory sequence; wherein Tm1 and Tm2are higher than the annealing temperature associated with thepolynucleotide amplification reaction.

Tagging

In this method, a nucleotide tag sequence (“tag sequence” or “NTS”) isassociated with the target nucleotide sequence (TNS), in a processreferred to as “tagging.” In one embodiment, without limitation, the tagsequence is associated with the target nucleotide sequence in anamplification reaction. For example, the TNS can be amplified using thepolymerase chain reaction (PCR) in which a first (e.g., “forward”)primer includes the nucleotide tag sequence 5′ to a target specificportion, resulting in an amplicon containing both the tag sequence andthe TNS (the tag sequence being 5′ and adjacent to the NTS). In general,the amplification reaction uses a second (e.g., “reverse”) primer.

In specific embodiments, the invention provides an amplification methodfor introducing each tag nucleotide sequence into one or more targetnucleic acid(s). The method entails amplifying the one or more nucleicacid(s), typically in a plurality of samples. The samples can differfrom one another in any way, e.g. the different samples can be fromdifferent tissues, subjects, environmental sources, etc. The tagsequence can be introduced as part of a tagging oligonucleotide. In anamplification reaction, e.g. PCR, the tagging oligonucleotide canfunction as a tagging primer, including a target nucleotide recognitionsequence and a nucleotide tag. The recognition can be encoded by partialor complete complementarity between the target nucleotide sequence andthe target nucleotide recognition sequence. Further, the nucleotide tagscan be chosen in association with the target nucleotide recognitionsequence(s) and can encode the target nucleotide sequence(s) in thetarget nucleic acid(s). A reverse primer flanking the sequence ofinterest can be provided.

The tag sequence can be incorporated immediately adjacent to the targetspecific sequence or with limited number of linker nucleotides inbetween. The number of linker nucleotides is preferably less than 25,more preferably less than 10, still more preferably less than 5. Inparticular embodiments, the probe oligonucleotide can be rescued fromthe regulatory oligonucleotide by hybridization to the tagged nucleicacid target(s). The hybridization can be directed to the nucleotide tagon the tagged target nucleic acid(s) that is recognized by a nucleotidetag recognition sequence on the probe oligonucleotide.

According to the present invention, the tag sequence and the TNS definea composite sequence stretch (CSS), which is more generally referred toas the “tagged target nucleic acid sequence”, and sometimes referred toas “tagged polynucleotide target”. Amplicons comprising the taggedtarget nucleic acid sequence can be double or single stranded.

Tagging primers, containing a target nucleotide recognition sequence anda tag sequence, are used to associate the nucleotide tag sequence intothe “tagged target nucleic acid sequence. Preferably, the tagging primeris in the range of 15-60 nucleotides in length. More preferably, thetagging primer is in the range of 18-45 nucleotides in length. Theprecise sequence and length of the tagging primer depends in part on thenature of the target nucleotide sequence to which it binds. The sequenceand length may be varied to achieve appropriate annealing and meltingproperties for a particular embodiment. Preferably, the tagging primerhas a melting temperature, Tm in the range of 50-85° C. More preferably,the tagging primer has a melting temperature, Tm in the range of 60-75°C. In particular examples, the sequence and the length of the targetnucleotide recognition sequence may be varied to achieve appropriateannealing and melting properties with the probe.

In embodiments in which the amplicon product of the amplificationreaction is double stranded, the first strand will contain the tagsequence and the TNS, and the complementary strand will contain thecomplement of the sequences in the first strand. For purposes ofclarity, the discussion below refers to the tag sequence and TNS, but itwill be appreciated that equivalent assays may be carried out using thecomplementary sequences. One of skill guided by this disclosure willimmediately recognize how to conduct the assays of the invention bydetecting either strand, with appropriate adjustments to primer andprobe sequences.

It will be appreciated that, depending on the nature of the step inwhich the tag sequence is associated with the target nucleotidesequence, the tagged target nucleic acid sequence can include additionalsequence elements, for example if a forward primer includes sequences inaddition to the tag sequence and the target specific portion and/or areverse primer includes sequences in addition to target specificsequences.

Probe Oligonucleotide

The invention further relates to a probe oligonucleotide (sometimesreferred to as “oligonucleotide probe”) that associates with a portionof the tagged target nucleic acid sequence (CSS). That is, the probeoligonucleotide comprises a “nucleotide tag recognition sequence”portion complementary to the nucleotide tag sequence portion of thetagged target nucleic acid sequence, such that the oligonucleotide probecan hybridize to the tagged target nucleic acid sequence and act as aprimer in an amplification reaction. The nucleotide tag recognitionsequence can be partially or completely identical to the nucleotide tagsequence or its complement. The probe oligonucleotide generally alsocontains a regulatory sequence, usually 5′ to the nucleotide tagsequence, as discussed below.

In one embodiment, the nucleotide tag recognition sequence of the probeoligonucleotide hybridizes to the complement of the nucleotide tagsequence. That is, the nucleotide tag sequence may be at the 5′ end ofone strand of the tagged target nucleic acid sequence (or “taggedpolynucleotide”), and the probe oligonucleotide may hybridize to thecomplement of the nucleotide tag sequence, at the 3′ end of the secondstrand of the tagged polynucleotide.

Preferably, the probe oligonucleotide is in the range of 15-60nucleotides in length. More preferably, the probe oligonucleotide is inthe range of 18-45 nucleotides in length. The precise sequence andlength of an probe oligonucleotide depends in part on the nature of thenucleotide tag to which it binds. Typically, the sequence of the probeoligonucleotide that is complementary to the targeted taggedpolynucleotide(s), is longer than the regulatory sequence of the probeoligonucleotide. The overall sequence and length may be varied toachieve appropriate annealing and melting properties for a particularembodiment. The melting temperature of the probe oligonucleotide may begreater than 95° C. The melting temperature of the probe oligonucleotidecan fall within a range of, 50-85° C., 55-80° C., 60-75° C., 65-70° C.,75° C., 60-120° C., 75-115° C. or more or it can fall within a rangehaving one of these values as endpoints (e.g. 50-75° C.). Preferably,the probe oligonucleotide has a melting temperature, Tm in the range of55-85° C. More preferably, the probe oligonucleotide has a meltingtemperature, Tm in the range of 65-75° C., ever more preferably >75° C.In some embodiments the calculated Tm for the probe oligonucleotide maybe >100° C. In particular examples, the nucleotide tag recognitionsequence and length may be varied to achieve appropriate annealing andmelting properties in the initial cycles of an amplification reactionwhen the probe is first incorporated into the polynucleotide.

Amplification of the Tagged Target Nucleic Acid Sequence by the ProbeOligonucleotide

In some embodiments the tagged target nucleic acid sequence (or aportion thereof) is amplified in a PCR amplification reaction using theprobe oligonucleotide as a primer. Generally the amplification reactionincludes a 3′ (reverse) primer. It will be recognized that, when theprobe oligonucleotide comprises a regulatory sequence, the product ofthe amplification will include the regulatory sequence, the nucleotidetag sequence, and the target nucleotide sequence.

The probe oligonucleotide can be further incorporated into longernucleic acid constructs in a tagged target nucleic acid dependentmethod. For example, the probe oligonucleotide can be ligated to anothernucleic acid facilitated by proximity via hybridization to the taggedtarget nucleic acid(s). More often, the probe oligonucleotide can serveas a primer in an amplification reaction where it is incorporated to thetagged target nucleic acid(s).

The PCR amplification reaction is characterized by an annealingtemperature Ta (see below). According to the present invention, themelting temperature of the probe oligonucleotide (Tm1) is greater thanthe Ta of the amplification reaction. In some embodiments Tm1 is atleast 1° C., at least 2° C., at least 3° C., at least 4° C., at least 5°C., at least 6° C., at least 7° C., at least 8° C., at least 9° C., atleast 10° C., at least 11° C., at least 12° C., at least 13° C., atleast 14° C., at least 15° C., at least 16° C., at least 17° C., atleast 18° C., at least 19° C., at least 20° C., at least 21° C., atleast 22° C., at least 23° C., at least 24° C., at least 25° C., atleast 35° C. or at least 50° C. higher than the annealing temperature.In some embodiments, Tm1 is at least 50° C. higher than the annealingtemperature (Ta). In some embodiments Tm1 is at least 25° C. higher thanTm2.

The PCR amplification reaction is carried out in the presence of aregulatory oligonucleotide, as discussed below.

Regulatory Oligonucleotide

Properties of the Regulatory Oligonucleotide

The invention relates to a regulatory oligonucleotide, which comprises(1) a sequence segment complementary to the regulatory sequence of theprobe oligonucleotide and (2) a tail segment located 5-prime to thesequence segment. Annealing of the sequence segment of the regulatoryoligonucleotide to the regulatory sequence of the probe oligonucleotidecompetes with the association of the probe oligonucleotide and thetagged target nucleic acid sequence (or “CSS”) during the amplificationreaction.

Preferably, the regulatory oligonucleotide is in the range of 6-60nucleotides in length. More preferably, the regulatory oligonucleotideis in the range of 15-45 nucleotides in length. Even more preferably,the regulatory oligonucleotide is in the range of 18-30 nucleotides inlength. In some embodiments the regulatory oligonucleotide may comprisenucleotides that flank the sequence segment (e.g., 1, 2, 3, 4, 5, 6, 7,8, 9, 10 or more than 10 nucleotides). Preferably, the 3′ terminalnucleotide of the regulatory oligonucleotide is blocked or renderedincapable of extension by a nucleic acid polymerase. Such blocking isconveniently carried out by the attachment of a reporter or quenchermolecule to the terminal 3′ carbon of the probe oligonucleotide by alinking moiety. For purposes of this disclosure we will refer to aregulatory oligonucleotide as having a “quencher” moiety, but it will berecognized that a reporter may be used.

In some embodiments, the length of the regulatory oligonucleotide is inthe range of 15-60 nucleotides, more preferably, in the range of 15-45nucleotides in length, and even more preferably in the range of 18-30nucleotides in length.

Properties of the Sequence Segment

In some embodiments, sequence segment comprises all or most (e.g., atleast 80% or at least 90%) of the length of the regulatoryoligonucleotide. In some embodiments, the length of the sequence segmentis at least 40%, at least 50%, at least 60% or at least 70% of thelength of the regulatory oligonucleotide. In some embodiments, sequencesegment is in the range of 6-50 nucleotides in length, more preferably,in the range of 15-45 nucleotides in length, and even more preferably inthe range of 18-30 nucleotides in length. The precise sequence andlength of the regulatory oligonucleotide depends in part on the natureof the probe oligonucleotide to which it binds. The sequence and lengthmay be varied to achieve appropriate annealing and melting propertiesfor a particular embodiment.

In various embodiments, the concentration of the regulatoryoligonucleotide can be in excess of the probe oligonucleotide. In someembodiments, the concentration of the regulatory oligonucleotide can beadjusted according to the total nucleic acid(s) in the reaction. Theregulatory oligonucleotide can be supplied in excess of at least 10%,50%, 100%, 500%, 1000% or more over the oligonucletide probe or thetotal nucleic acid(s) in the reaction.

Properties of the Regulatory Oligonucleotide Tail Segment

Inclusion of the tail segment provides certain advantages over othermethods, as illustrated in FIGS. 2A-2B. The tail segment of theregulatory oligonucleotide is designed so that, when the sequencesegment of the regulatory oligonucleotide is hybridized to the probeoligonucleotide, the tail segment is unhybridized. Thus, when theregulatory oligonucleotide is hybridized to the probe oligonucleotidethe resulting complex is partly double-stranded and partiallysingle-stranded as shown in FIGS. 2A-2B. The double-stranded portioncomprises the regulatory sequence of the probe annealed to thecomplementary sequence of the regulatory oligonucleotide. A firstsingle-stranded portion comprises the unhybridized portion of the probeoligonucleotide 3-prime (3′) to the annealed portion, including thenucleotide tag recognition sequence. A second single-stranded portioncomprises the unhybridized tail portion of the regulatoryoligonucleotide 5-prime (5′) to the annealed portion.

Inclusion of the unpaired sequence in the regulatory oligonucleotide canhelp prevent digestion of the hybridized regulatory oligonucleotide. Asillustrated in FIG. 2B, a regulatory oligonucleotide lacking a tailsegment (i.e., a “tail-less regulatory oligonucleotide) is digested bythe action of the Taq polymerase generally used in PCR amplification orother polymerases with 5′→3′ exonuclease activity. As illustrated inFIG. 2A, when a regulatory oligonucleotide comprising a 5-prime tailsegment is used, digestion of the oligonucleotide is reduced oreliminated and strand displacement is increased. As illustrated in FIG.2A (bottom) the displaced regulatory oligonucleotide is available tohybridize to free probe oligonucleotide, quenching the reporter moiety,and reducing background fluorescence. In contrast, the tail-lessregulatory oligonucleotide is digested (FIG. 2B, bottom) and is notavailable to hybridize to free probe oligonucleotide.

The length of the tail segment can vary, e.g., from 3-50 bases inlength. In some embodiments the tail is 4-10 bases in length, typically6-8 bases in length. Typically the tail is at least about 50% GC, oftenat least about 60% GC, more often at least about 70% GC, and most oftenat least about 80% GC. It will be recognized that the sequence of thetail sequence is selected so that it does not form a double strand withthe corresponding region of the probe oligonucleotide. Thus, the tailsegment is not exactly (i.e., 100%) complementary to the correspondingregion of the probe oligonucleotide. Preferably, none of the positionsin the tail segment contains a base that pairs with the base at thecorresponding region of the probe oligonucleotide, assuming A pairs withT and G pairs with C. That is, preferably the bases at correspondingpositions of the probe oligonucleotide and regulatory oligonucleotideare noncomplementary. Preferably none of the corresponding positionscontains a complementary base (i.e., 100% noncomplementarity). In someembodiments there is at least 85% noncomplementarity, at least 70%noncomplementarity or at least 50% noncomplementarity.

Properties of Polymerases

By selecting a polymerase with minimal or no endonuclease activity, andpossessing sufficient strand displacement activity, the regulatoryoligonucleotide is displaced by the polymerase rather than digested.

A preferred DNA polymerase for the PCR amplification steps of thepresent method is (a) thermostable and (b) lacks, or has reduced, 5′nuclease activity. A preferred DNA polymerase for the PCR amplificationsteps of the present method additionally exhibits strong stranddisplacement activity. Polymerases useful in such reactions are readilyavailable and include those described in U.S. Pat. No. 5,108,892, whichis incorporated by reference in its entirety, as well as those enzymesdescribed in Lawyer et al., 1993, Genome Res. 2, 275-278, 1993, and Konget al., 1993, J. Biol. Chem. 268, 1965-1975, both incorporated herein byreference.

Taq polymerase (DNA polymerase I from Thermus aquaticus) is commonlyused in PCR reactions. Taq polymerase catalyzes the hydrolysis ofpolynucleotides bound to the template DNA strand as it translocatesalong this strand. Lyamichev et al. demonstrated that Taq polymerasecan, when approaching a “frayed” DNA duplex with a free 5′ arm, cleavethe 5′ arm endonucleolytically near the end of the duplex (Lyamichev etal., 1993, Science 260, 778-783). In addition to the oligonucleotidesresulting from such cleavage, Taq polymerase also generatesmononucleotides resulting from 5′ exonuclease digestion of the DNAstrand from which the 5′ arm is cleaved (Holland et al., 1991, Proc.Natl. Acad. Sci. USA 88:7276-7280). Accordingly, Lyamichev at al. coinedthe term “5′ nuclease” to refer to the 5′43′ endonuclease andexonuclease activities of Taq polymerase taken together (Lyamichev etal., 1993, Science 260, 778-783). Native Taq polymerase is known anddescribed in, for example, U.S. Pat. No. 5,108,892.

The 5′ nuclease and polymerase activities of Taq polymerase are thoughtto arise from separate domains of the enzyme. The N-terminal domain(amino acids ˜1-288) has been shown to have 5′ nuclease activity byitself (Lyamichev et al. 1999, Proc. Natl. Acad. Sci. USA 96,6143-6148). Conversely, the C-terminal domain (amino acids ˜289-832,known as the “Stoffel fragment”) has polymerase activity but vastlyreduced 5′→3′ exonuclease activity (See Lawyer at al., 1993, Genome Res.2:275-278). However, greater fidelity is observed for each activity withthe full enzyme than with the respective domain in isolation.

Researchers have sought to engineer versions of Taq polymerase that lack5′ nuclease activity, because such activity can degrade primers used insequencing (Burke et al. U.S. Pat. No. 5,108,892), or interfere withsignal production in some kinds of qPCR (Wilhelm et al., 2001,BioTechniques 30:1052-1062). Burke and co-workers (U.S. Pat. No.5,108,892) harvested Taq polymerase from T. aquaticus cells and allowedit to undergo limited proteolysis, which apparently caused thedeactivation of the N-terminal domain. Wurst and Qiu. U.S. Pat. No.6,130,045, replaced the N-terminal domain with only 9-15 amino acids,and expressed the mutant protein recombinantly. Other examples aredescribed in Fu (U.S. Patent Application Publication 2012/0115145).Thus, 5′ nuclease activity can be eliminated by deleting, truncating,mutating, or otherwise inactivating the N-terminal domain, so long asthe C-terminal domain is preserved.

In order for a translocating DNA polymerase to displace anoligonucleotide bound to the template strand, without hydrolyzing theoligonucleotide, the polymerase should not only lack 5′ nucleaseactivity but also possess strand displacement activity (Fu, U.S. PatentApplication Publication 2012/0115145, Kong et al., 1993, J. Biol. Chem.268, 1965-1975). Assays for strand displacement activity are known. See,e.g., U.S. Pat. No. 5,744,312 and Kong et al., 1993, J. Biol. Chem. 268,1965-1975. Examples of polymerases with strong strand displacementactivity include Vent polymerase (Kong et al., 1993, J. Biol. Chem. 268,1965-1975; Combs et al. “Purified thermostable DNA polymerase obtainablefrom thermococcus litoralis”, U.S. Pat. Nos. 5,210,036 and 5,322,785),Burke's enzyme (U.S. Pat. No. 5,108,892), and the Stoffel fragment(Lawyer et al., 1993, Genome Res. 2, 275-278, 1993).

Among those available commercially polymerases are aTaq polymerase(Promega; Product code M1245), Titanium Taq (Clontech), Pfu polymerase(many vendors), and Thermococcus litoralis (Tli; a.k.a. “Vent”) DNApolymerase (Kong et al., 1993, J. Biol. Chem. 268, 1965-1975). Ventpolymerase is also notable for its strong strand displacement activity,and would be suitable for performing PCR in the presence of a probeoligonucleotide that hybridizes to the target sequence, without causinghydrolysis of the oligonucleotide. For example, Pfu polymerase andThermococcus litoralis (Tli; a.k.a. “Vent”) polymerase lack thisactivity. See Table 4 of Lawyer et al., 1993, Genome Res. 2: 275-278,1993). Thermococcus litoralis DNA polymerase is commercially availablefrom NEB in exo+ and exo-versions, where “exo” refers to 3′→5′exonuclease activity. The exo− version has greater strand displacementactivity.

In one embodiment, the assay of the invention is carried out using a DNApolymerase with strong strand displacing activity (e.g., specificactivity at least 90%, preferably at least 100% as great as Tlipolymerase; Kong et al., 1993, J. Biol. Chem. 268, 1965-1975) and low 5′nuclease activity (e.g., endo- and exo-nuclease specific activity nogreater than that of Tli polymerase). In one embodiment, the assay ofthe invention is carried out using a DNA polymerase with stranddisplacing activity greater than that of native Taq polymerase (e.g., atleast 150% as much) and less 5′-endo- and 5′-exo-nuclease specificactivity than native Taq polymerase (no greater than 50% as much).

Each reference cited in this “properties of polymerase” section ishereby incorporated by reference in its entirety and specifically forits description of DNA polymerases.

Melting Temperature of the Regulatory Oligonucleotide

The melting temperature of the regulatory oligonucleotide (Tm2) ismeasured or calculated based on the sequence segment complementary tothe regulatory sequence of the probe oligonucleotide, including the tailsegment.

The melting temperature of the regulatory oligonucleotide (Tm2) can fallwithin a range of, 45-85° C., 50-80° C., 55-75° C., 60-70° C., 65-75° C.or it can fall within a range having two of these values as endpoints(e.g. 50-75° C.). Preferably, the regulatory oligonucleotide has amelting temperature, Tm in the range of 50-85° C. More preferably, theregulatory oligonucleotide has a melting temperature, Tm in the range of60-75° C. In particular examples, the sequence and the length of thesegment recognizing the regulatory sequence may be varied to achieveappropriate annealing and melting properties with the probe. In someembodiments, a competitive auxiliary sequence may be added to increasethe specificity of the probe oligonucleotide for the tagged targetnucleic acid.

In one embodiment of the present invention, the melting temperature ofthe regulatory oligonucleotide (Tm2) is greater than the Ta of theamplification reaction. In one embodiment the melting temperature of thesequence segment complementary to the regulatory sequence of the probeoligonucleotide (Tm2) is greater than the Ta of the amplificationreaction. In some embodiments Tm2 is at least 1° C., at least 2° C., atleast 3° C., at least 4° C., at least 5° C., at least 6° C., at least 7°C., at least 8° C., at least 9° C., at least 10° C., at least 11° C., atleast 12° C., at least 13° C., at least 14° C., at least 15° C., atleast 16° C., at least 17° C., at least 18° C., at least 19° C., atleast 20° C., at least 21° C., at least 22° C., at least 23° C., atleast 24 or at least 25° C. higher than the annealing temperature.

Auxiliary Sequence

The regulatory oligonucleotide can have an auxiliary sequence that actsas a competitive sequence against the target nucleic acid/probeoligonucleotide hybridization. When the probe oligonucleotide and theregulatory oligonucleotide are aligned along the regulatory sequence,the auxiliary sequence segment can at least partially overlap with theprobe oligonucleotide, more typically with the nucleotide tagrecognition sequence. That is, the regulatory oligonucleotide cancomprise a sequence complementary to both the regulatory sequence of theprobe oligonucleotide and at least a portion of the nucleotide tagrecognition sequence of the probe oligonucleotide. Put differently, thesequence segment of the regulatory oligonucleotide can be complementaryto the regulatory sequence and at least a portion of the nucleotide tagrecognition sequence of the probe oligonucleotide. The degree ofcomplementarity between the auxiliary sequence and the probeoligonucleotide can be adjusted to regulate specificity. In embodiments,wherein the probe oligonucleotide is incorporated into the taggedpolynucleotide in an amplification reaction, the auxiliary sequence cancompete against non-specific sites, more specifically untagged nucleicacid(s) even in the initial cycles of an amplification reaction. Thehybridization of the regulatory oligonucleotide and the probeoligonucleotide along the regulatory sequence can enhance thehybridization of the auxiliary sequence to the probe oligonucleotide,since the auxiliary sequence would be presented at increased localconcentrations compared to free nucleic acid(s). In addition, theconcentration of the regulatory oligonucleotide, and thus the auxiliarysequence, can be adjusted to allow it to compete effectively againstuntagged nucleic acid(s). In specific embodiments, the regulatoryoligonucleotide can be provided at 1.5 to 4-fold excess, 1 to 10-foldexcess, 4 to 10-fold excess, 1.5 to 50-fold excess, 4 to 50, 100-foldexcess or any other range having any of these values as endpoints (e.g.,1.5 to 10-fold excess). With these advantages, the auxiliary sequencecan regulate specificity at even low to zero complementarity for theprobe oligonucleotide. At low to no complementarity between theauxiliary sequence and the probe oligonucleotide, the probeoligonucleotide hybridization to the tagged nucleic acid(s) wouldsuccessfully outcompete the auxiliary sequence on the regulatoryoligonucleotide.

Further, a quencher sequence can be incorporated into the regulatoryoligonucleotide sequence to increase quenching. In preferred embodimentsone or more deoxyguanosine nucleotides will be incorporated to thequencher sequence around the hybridization site of the reporter moleculeon the probe oligonucleotide. In some embodiments, a deoxyguanosine tailcan be added to the quencher sequence, 3′ to the regulatory sequencehybridization.

Correspondence of Signal and the Presence of the Target Sequence

Association with the regulatory oligonucleotide affects the signalassociated with the probe oligonucleotide. Accordingly, the interactionof the probe oligonucleotide with the CSS prevents the probeoligonucleotide from hybridizing to the regulatory oligonucleotide. As aresult, a change in probe oligonucleotide-associated signal aids in thedetection of a target nucleotide sequence.

The incorporation of the tag sequence is designed to be dependent on thepresence of the specific TNS. As a result, the present invention linksthe presence of a specific nucleotide sequence (i.e., a specific targetnucleic acid sequence) in a sample to a change in signal. The signal canbe acquired before and after the sample is interrogated with thedetection method of the present invention. Accordingly, a change insignal is interpreted to be associated with the presence of a specificTNS. Further, the present invention also relates to monitoring theamplification of a target polynucleotide sequence. Accordingly, thepresent invention relates to a method for monitoring nucleic acidamplification of a target sequence by following the change in signalover time.

In various embodiments of the invention, the changed signal associatedwith the incorporation of the probe oligonucleotide to a taggednucleotide relates to the release of the probe oligonucleotide from aregulatory oligonucleotide. The association of the regulatoryoligonucleotide to unincorporated probe oligonucleotide forms areporter/quencher pair such that a possible signal is quenched underconditions suitable for this association. The incorporation of the probeoligonucleotide to a tagged target nucleic acid disrupts the formationof such a reporter/quencher pair resulting in a change in signal. Invarious embodiments, the probe oligonucleotide is labeled with thereporter molecule and the regulatory oligonucleotide is labeled with aquencher molecule. Exemplary reporter/quencher pairs comprisefluorescence dyes and their quenchers.

In some embodiments, a plurality of probe oligonucleotides will bespecifically directed to different tag sequences. The signal associatedwith each tag sequence is differentiated by linking each probeoligonucleotide recognizing a particular nucleotide tag to a specificreporter or quencher.

In the present assay approach, when a complementary target sequence ispresent, hybridization of the probe to the complementary target sequencedisrupts the hybridization of the regulatory oligonucleotide to theprobe, wherein the quencher molecule is no longer close enough to thereporter molecule to quench the reporter molecule. As a result, theprobes provide an increased fluorescent signal when hybridized to atarget sequence than when unhybridized.

Annealing Temperature

During the annealing phase of a polynucleotide amplification reaction,the primers anneal to polynucleotides to prime an elongation reaction atthe elongation temperature. The “annealing temperature” of anamplification reaction is usually determined experimentally to obtainhighest yields with desired specificities. Generally, higher annealingtemperatures increase specificity for the targeted polynucleotide. Thefraction of annealed primers at a target site in a reaction directlyaffects overall yield and depends on many factors, including competingsites in the target and other polynucleotides in the reaction, theannealing time, the melting temperature associated with thecomplementary region of the primer with the target site and theannealing temperature. Higher annealing temperatures affect primerbinding energies to non-specific competing sites in the reaction andthus may shift this population of primer to specific target sites.Higher annealing temperatures also increase the fraction of singlestranded target polynucleotides in the reaction that are available forprimer binding. However, higher annealing temperatures have a disablingeffect on specific primer binding to target sites by affecting thebinding free energy for this interaction. Desired annealing temperaturesassist the reaction yield by increasing the fraction of annealed primersto the targeted site.

A “yielding annealing temperature” falls in a temperature range thatresults in the amplification of desired targets at a rate higher thanthe amplification of untargeted polynucleotide sequences in thereaction. A yielding annealing temperature for each amplificationreaction can be independently chosen. Yielding annealing temperaturescan be chosen from a range of temperatures, for example the annealingtemperature can within a range of 15° C.-80° C., 30° C.-75° C., 40°C.-75° C., 50° C.-72° C., 60° C.-64° C., 55° C.-62°, 63° C., 64° C., 65°C. or can fall within any range having one of these temperatures asendpoints (e.g. 50° C.-62° C.). In some embodiments, the amplificationreaction is PCR.

The hybridization specificity of an oligonucleotide to a target site isincreased by decreasing oligonucleotide binding to non-specific sites.Non-specific target sites are usually sites with lower complementarity,but for the purpose of the reaction, they are generally sites whereoligonucleotide binding is not desired.

There are several techniques addressing the increased specificityrequirements at a given annealing temperature. These techniques allowthe use of lower annealing temperatures and employ competitiveinhibitors for the binding of a primer and a target nucleic acid. Puskaset al., Genome Research 5:309-311 (1995) and Harry et al.,BioTechniques, 24:445-450 (1998), which are hereby incorporated byreference, provide primers that are complementary to a target nucleotidesequence and oligonucleotides that are partially complementary to saidtarget nucleotide sequence and are 3′ modified to prevent elongation.These oligonucleotides increase specificity by occupying non-specificsites that the primers would have annealed to and divert the primerpopulation towards the target nucleotide sequence instead. Due to theirpartial complementarity to the target nucleotide sequence, the primersare able to compete successfully against the partially complementaryoligonucleotides for the target nucleotide sequences. Kong et al.,Biotechnology Letters, 26:277-280 (2004), which is hereby incorporatedby reference, employs as competitive inhibitors, oligonucleotides thatare partially complementary to the primers. These oligonucleotidescompete successfully against non-specific sites for the primers andincrease specificity by making the primers less available for saidsites. Due to their reduced complementarity, the target nucleotidesequences can outcompete said oligonucleotides for primer binding.

The various oligonucleotides can be selected to achieve a desired degreeof specificity at the chosen annealing temperatures. The targetnucleotide recognition sequence on the tagging primer(s) canspecifically anneal to a target nucleotide sequence under suitableconditions and at the chosen annealing temperature. The conditions canbe selected such that the primer annealing will be sensitive tovariations in the target nucleotide sequence. Generally, nucleotidemismatches towards the 3′ end of a primer greatly affect elongation froma primer. To differentiate between sequence variants, the primer can bedesigned such that the 3′ end of it would be directed to the polymorphicsite. Alternatively, sequences with higher melting temperatures can bechosen achieving less specific annealing to a broader variety of targetnucleotide sequences.

With high specificity sequences, the primer can effectivelydifferentiate between polymorphisms in the target nucleic acid(s). Thepolymorphisms can encompass single or multiple nucleotide changes at oneor more polymorphic site(s). The changes at the polymorphic site(s) caninvolve deletions, insertions and substitutions of single all multiplenucleotides. Elongation from the primer is particularly sensitive to thehybridization stability at the 3′ end of the primer. Primers designed toalign with a polymorphic site at their 3′ end are thus especially usefulto differentiate between various alleles.

Tagging and Detection Reactions

The target nucleotide tagging and detection can be conducted in separatereactions. Alternatively, these two steps can be performed in a commonreaction volume. A double amplification method can be used toincorporate a tagging primer comprising a target nucleotide recognitionsequence and a nucleotide tag and an oligonucleotide primer/probecomprising a nucleotide tag recognition sequence, a regulatory sequenceand a signal moiety.

Reporter and Quencher Pairs

In various embodiments, the invention provides one or more pairs of aprobe oligonucleotide and a regulatory oligonucleotide that specificallyanneal to each other, wherein one of them is labeled with a reportermolecule and the other with a quencher molecule of a reporter-quencherpair. When the probe oligonucleotide and the regulatory oligonucleotideare aligned along the regulatory sequence, the reporter molecule andquencher molecule are positioned on the oligonucleotides sufficientlyclose to each other such that whenever the reporter molecule is excited,the energy of the excited state nonradiatively transfers to the quenchermolecule where it either dissipates nonradiatively or is emitted at adifferent emission frequency than that of the reporter molecule.Typically, the probe oligonucleotide will comprise the reporter moleculeand the regulatory oligonucleotide will comprise the quencher molecule,however this positioning can be reversed and this modifications will beapparent to practitioners skilled in this art.

In some embodiments the assay of the invention uses an probeoligonucleotide containing a reporter molecule and a regulatoryoligonucleotide containing a quencher molecule, said reporter andquencher molecules being members of a reporter-quencher pair. Theregulatory oligonucleotide comprises a sequence that hybridizes to aregulatory sequence in the probe oligonucleotide. The probeoligonucleotide specifically anneals to a region of a target taggedpolynucleotide with a target nucleotide sequence, such that thenucleotide tag recognition sequence hybridizes to a nucleotide tag inthe tagged polynucleotide. The nucleotide tag is typically incorporatedto the target polynucleotide using a tagging primer comprising anucleotide tag sequence and a target nucleotide recognition sequence,where the target nucleotide recognition sequence hybridizes to thetarget nucleotide sequence. An amplification reaction, typically PCR, iscarried out to incorporate the tagging primer into the targetpolynucleotide (i.e., producing amplicons containing both the nucleotidetag sequence and the target nucleotide sequence).

When the regulatory oligonucleotide hybridizes to the probeoligonucleotide along the regulatory sequence, the reporter molecule andquencher molecule are positioned sufficiently close to each other suchthat whenever the reporter molecule is excited, the energy of theexcited state nonradiatively transfers to the quencher molecule where iteither dissipates nonradiatively or is emitted at a different emissionfrequency than that of the reporter molecule. During strand extension bya DNA polymerase, the probe oligonucleotide anneals to the template andacts as a primer. As a result of the probe is incorporated into anamplicon and the reporter molecule is effectively separated from thequencher molecule such that the quencher molecule is no longer closeenough to the reporter molecule to quench the reporter molecule'sfluorescence. Thus, as more and more probe oligonucleotides areincorporated into double-stranded polynucleotides during amplification,larger numbers of reporter molecules are released from close proximityinteractions with quencher molecules, thus resulting in an increasingnumber of unquenched reporter molecules which produce a stronger andstronger fluorescent signal. The detection is typically carried outunder conditions wherein higher than a desired fraction ofunincorporated probe oligonucleotide is hybridized to the regulatoryoligonucleotide. During any stage of the detection, the amount of theunincorporated probe oligonucleotide that is hybridized to theregulatory oligonucleotide is preferably greater than 50%, 80%, 90%,95%, 99%, 99.5%, 99.9%, 99.95% or more of the total unincorporated probeoligonucleotide. The detection conditions are also selected such thatthe amount of unincorporated probe oligonucleotide that is notassociated to the regulatory oligonucleotide is low compared to theincorporated probe oligonucleotide. During any stage of the detection,the amount of unincorporated oligonucleotide that is not associated tothe regulatory oligonucleotide is preferably less than 50%, 20%, 10%,5%, 1%, 0.5%, 0.1%, 0.05% or less of the incorporated probeoligonucleotide.

In various embodiments, the invention provides a detection method forone or more target nucleic acid(s), typically one or more targetpolynucleotide(s), using one or more probe oligonucleotide(s). The probeoligonucleotide's signal can be modulated by rescuing the probe from aregulatory oligonucleotide recognizing a regulatory sequence on theprobe. The recognition can be encoded in a sequence segment in theregulatory oligonucleotide with partial or complete complementarity tothe regulatory sequence on the probe oligonucleotide.

Various factors influence the utility of reporter-quencher moleculepairs in hybridization and amplification assays. The first factor is theeffectiveness of the quencher molecule to quench the reporter molecule.This first factor, herein designated “RQ⁻”, can be characterized by theratio of the fluorescent emissions of the reporter molecule to thequencher molecule when the probe is not hybridized to a perfectlycomplementary polynucleotide. That is, RQ⁻ is the ratio of thefluorescent emissions of the reporter molecule to the energy that istransferred to the quencher molecule when the probe oligonucleotide ishybridized to the regulatory oligonucleotide. Influences on the value ofRQ⁻ include, for example, the particular reporter and quencher moleculesused, the spacing between the reporter and quencher molecules in thehybridized complex, nucleotide sequence-specific effects, and the degreeof flexibility of structures, and the presence of impurities. A relatedquantity RQ⁺, refers to the ratio of fluorescent emissions of thereporter molecule to the energy that is transferred to quencher moleculewhen the probe oligonucleotide is hybridized to a complementarypolynucleotide.

A second factor is the efficiency of the probe to hybridize to acomplementary polynucleotide. This second factor depends on the probe'smelting temperature, T_(m), the presence of a secondary structure in theprobe or target polynucleotide, the temperature of the reaction, andother reaction conditions.

A third factor is the efficiency of the regulatory oligonucleotide tohybridize to the probe oligonucleotide.

This third factor depends on the regulatory oligonucleotide's meltingtemperature, T_(m), the degree of complementarity between the regulatoryoligonucleotide and the probe oligonucleotide, the presence of asecondary structure in the probe or regulatory oligonucleotide, thetemperature of the reaction, and other reaction conditions.

A fourth factor is the oligonucleotide sequence in the vicinity of thereporter molecule. Depending on the sequence, the fluorescence intensityof the probe is either increased or decreased by hybridization. A strongdegree of quenching is observed by hybridization to sequences containingdeoxyguanosine nucleotides (Gs), giving a sequence specific decrease inflorescence. For additional discussion of this effect, see Crocket etal., Analytical Biochemistry, 290:89-97 (2001) and Behlke et al.,Fluorescence Quenching by Proximal G-bases (available on the world wideweb at: http: double backslashcdn.idtdna.com/Support/Technical/TechnicalBulletinPDF/Fluorescence_quenching_by_proximal_G_bases.pdf).

Preferably, reporter molecules are fluorescent organic dyes derivatizedfor attachment to the terminal 3′ carbon or terminal 5′ carbon of theprobe oligonucleotide and the regulatory oligonucleotide via a linkingmoiety. Preferably, quencher molecules are also organic dyes, which mayor may not be fluorescent, depending on the embodiment of the invention.For example, in a preferred embodiment of the invention, the quenchermolecule is fluorescent. Generally whether the quencher molecule isfluorescent or simply releases the transferred energy from the reporterby non-radiative decay, the absorption band of the quencher shouldsubstantially overlap the fluorescent emission band of the reportermolecule. Non-fluorescent quencher molecules (NFQMs), such as Black Holequenchers, that absorb energy from excited reporter molecules, but whichdo not release the energy radiatively, are known in the art and may beused.

There is a great deal of practical guidance available in the literaturefor selecting appropriate reporter-quencher pairs for particular probes,as exemplified by the following references: Clegg (cited above); Wu etal. (cited above); Pesce et al., editors, Fluorescence Spectroscopy(Marcel Dekker, New York, 1971); White et al., Fluorescence Analysis: APractical Approach (Marcel Dekker, New York, 1970); and the like. Theliterature also includes references providing exhaustive lists offluorescent molecules and NFQMs, and their relevant optical propertiesfor choosing reporter-quencher pairs, e.g., Berlman, Handbook ofFluorescence Spectra of Aromatic Molecules, 2nd Edition (Academic Press,New York, 1971); Griffiths, Colour and Constitution of Organic Molecules(Academic Press, New York, 1976); Bishop, editor, Indicators (PergamonPress, Oxford, 1972); Haugland, Handbook of Fluorescent Probes andResearch Chemicals (Molecular Probes, Eugene, 1992) Pringsheim,Fluorescence and Phosphorescence (Interscience Publishers, New York,1949); and the like. Further, there is extensive guidance in theliterature for derivatizing reporter and quencher molecules for covalentattachment via common reactive groups that can be added to anoligonucleotide, as exemplified by the following references: Haugland(cited above); Ullman et al., U.S. Pat. No. 3,996,345; Khanna et al.,U.S. Pat. No. 4,351,760; and the like.

Exemplary reporter-quencher pairs may be selected from xanthene dyes,including fluoresceins, and rhodamine dyes. Many suitable forms of thesecompounds are widely available commercially with substituents on theirphenyl moieties which can be used as the site for bonding or as thebonding functionality for attachment to an oligonucleotide. Anothergroup of fluorescent compounds are the naphthylamines, having an aminogroup in the alpha or beta position. Included among such naphthylaminocompounds are 1-dimethylaminonaphthyl-5-sulfonate,1-anilino-8-naphthalene sulfonate and 2-p-touidinyl-6-naphthalenesulfonate. Other dyes include 3-phenyl-7-isocyanatocoumarin, acridines,such as 9-isothiocyanatoacridine and acridine orange;N-(p-(2-benzoxazolyl)phenyl)maleimide; benzoxadiazoles, stilbenes,pyrenes, and the like.

Preferably, reporter and quencher molecules are selected fromfluorescein and rhodamine dyes. These dyes and appropriate linkingmethodologies for attachment to oligonucleotides are described in manyreferences, e.g., Khanna et al. (cited above); Marshall, HistochemicalJ., 7:299-303 (1975); Menchen et al., U.S. Pat. No. 5,188,934; Menchenet al., European Patent Application 87310256.0; and Bergot et al.,International Application PCT/US90/05565. The latter four documents arehereby incorporated by reference.

In particular embodiments, fluorophores that can be used as detectablelabels for probes include, but are not limited to, rhodamine, cyanine 3(Cy 3), cyanine 5 (Cy 5), fluorescein, Vic™, LIZ™, Tamra™, 5-Fam™,6-Fam™, 6-HEX, CAL Fluor Green 520, CAL Fluor Gold 540, CAL Fluor Orange560, CAL Fluor Red 590, CAL Fluor Red 610, CAL Fluor Red 615, CAL FluorRed 635, and Texas Red (Molecular Probes). (Vic™, Liz™, Tamra™, 5-Fam™,6-Fam™ are all available from Applied Biosystems, Foster City, Calif.6-HEX and CAL Fluor dyes are available from Biosearch Technologies).

In particular embodiments, molecules useful as quenchers include, butare not limited to tetramethylrhodamine (TAMRA), DABCYL (DABSYL, DABMIor methyl red) anthroquinone, nitrothiazole, nitroimidazole, malachitegreen, Black Hole Quenchers®, e.g., BHQ1 (Biosearch Technologies), IowaBlack@ or ZEN quenchers (from Integrated DNA Technologies, Inc.), TIDEQuencher 2 (TQ2) and TIDE Quencher 3 (TQ3) (from AAT Bioquest).

There are many linking moieties and methodologies for attaching reporteror quencher molecules to the 5′ or 3′ termini of oligonucleotides, asexemplified by the following references: Eckstein, editor,Oligonucleotides and Analogues: A Practical Approach (IRL Press, Oxford,1991); Zuckerman et al., Nucleic Acids Research, 15: 5305-5321 (1987)(3′ thiol group on oligonucleotide); Sharma et al., Nucleic AcidsResearch, 19: 3019 (1991) (3′ sulfhydryl); Giusti et al., PCR Methodsand Applications, 2: 223-227 (1993) and Fung et al., U.S. Pat. No.4,757,141 (5′ phosphoamino group via Aminolink™ II available fromApplied Biosystems, Foster City, Calif.) Stabinsky, U.S. Pat. No.4,739,044 (3′ aminoalkylphosphoryl group); Agrawal et al., TetrahedronLetters, 31: 1543-1546 (1990) (attachment via phosphoramidate linkages);Sproat et al., Nucleic Acids Research, 15: 4837 (1987) (5′ mercaptogroup); Nelson et al., Nucleic Acids Research, 17: 7187-7194 (1989) (3′amino group); and the like.

Preferably, commercially available linking moieties are employed thatcan be attached to an oligonucleotide during synthesis, e.g., availablefrom Integrated DNA Technologies (Coralville, Iowa) or Eurofins MWGOperon (Huntsville, Ala.).

Rhodamine and fluorescein dyes are also conveniently attached to the 5′hydroxyl of an oligonucleotide at the conclusion of solid phasesynthesis by way of dyes derivatized with a phosphoramidite moiety,e.g., Woo et al., U.S. Pat. No. 5,231,191; and Hobbs, Jr., U.S. Pat. No.4,997,928.

By judicious choice of labels, analyses can be conducted in which thedifferent labels are excited and/or detected at different wavelengths ina single reaction. See, e.g., Fluorescence Spectroscopy (Pesce et al.,Eds.) Marcel Dekker, New York, (1971); White et al., FluorescenceAnalysis: A Practical Approach, Marcel Dekker, New York, (1970);Berlman, Handbook of Fluorescence Spectra of Aromatic Molecules, 2nded., Academic Press, New York, (1971); Griffiths, Colour andConstitution of Organic Molecules, Academic Press, New York, (1976);Indicators (Bishop, Ed.). Pergamon Press, Oxford, 19723; and Haugland,Handbook of Fluorescent Probes and Research Chemicals, Molecular Probes,Eugene (1992). The reporter and quencher molecules can be positioned onthe probe oligonucleotide and the regulatory oligonucleotidestrategically for a desired distance between these labels. Typically,the distance between the reporter and quencher molecules will beminimized to increase the effectiveness of the quencher molecule. Thelocation of the reporter and quencher molecules can be chosenstrategically such that upon hybridization of the probe oligonucleotideto the regulatory oligonucleotide, the reporter and quencher moleculesare less than 20 nm, 10 nm, 7.5 nm, 6 nm, 5 nm, 4 nm, 3 nm, 1 nm, 0.8nm, 0.6 nm, 0.4 nm or less apart. Preferably, the reporter and quenchermolecules can be positioned at complementary nucleotides in the contextof an probe oligonucleotide/regulatory oligonucleotide hybridizationalong the regulatory sequence. More preferably, the reporter and thequencher molecules can be positioned at the 5′ end of theoligonucleotide probe and the 3′ end of the regulatory olignucleotide.

Amplification Methods

In General

In illustrative embodiments, the same set of target nucleic acids can beamplified in each of two or more different samples. The samples candiffer from one another in any way, e.g., the samples can be fromdifferent tissues, subjects, environmental sources, etc.

The probe oligonucleotide can be provided in the amplification mixturein varying abundance compared to that of the tagging primer and/orreverse primer(s). More specifically, probe oligonucleotide can bepresent in excess of the tagging primer. The reverse primer in theamplification mixture, can be present, in illustrative embodiments, at aconcentration in excess of the tagging primer. For example, theconcentration of the probe oligonucleotide in the amplification mixturescan be at least 1.5-fold, at least 4-fold, at least 5-fold, at least10-fold, at least 15-fold, at least 20-fold, at least 25-fold, at least30-fold, at least 35-fold, at least 40-fold, at least 45-fold, at least50-fold, at least 100-fold, at least 500-fold, at least 10³-fold, atleast 5×10³-fold, at least 10⁴-fold, at least 5×10⁴-fold, at least10⁶-fold, at least 5×10⁶-fold, at least 10⁶-fold, or higher, relative tothe concentration of the tagging and/or reverse primer(s). Inillustrative embodiments, the tagging primer can be present in picomolarto nanomolar concentrations, e.g., about 500 nM to 5 μM, about 100 nM to5 μM, about 50 nM to 5 μM, about 10 nM to 5 μM, about 5 nM to 5 μM,about 1 nM to 10 μM, about 50 μM to about 500 μM, about 100 μM or anyother range having any of these values as endpoints (e.g., 10 nM to 50μM). Suitable, illustrative concentrations of probe oligonucleotide thatcould be used on combination with any of these concentrations of forwardprimer include about 10 nM to about 10 μM, about 25 nM to about 7.5 μM,about 50 nM to about 5 μM, about 75 nM to about 2.5 μM, about 100 nM toabout 1 μM, about 250 nM to about 750 nM, about 500 nM or any otherrange having any of these values as endpoints (e.g., 10 nM to 50 μM).

Each amplification mixture can be subjected to amplification to producetarget amplicons comprising tagged target nucleotide sequencescomprising the nucleotide tag. In certain embodiments, the nucleotidetag is selected so as to avoid substantial annealing to the targetnucleic acids. In such embodiments, the tagged target nucleotidesequences can include molecules having the following elements:5′-(nucleotide tag from the tagging primer)-(target nucleotidesequence)-3′.

In illustrative embodiments, the nucleotide tag sequence identifies aparticular polymorphic variant. Thus, for example, a set of T targetnucleic acids, each containing S polymorphic variants, can be amplified,where S and T are integers, typically greater than one. In suchembodiments, amplification can be performed separately for each targetnucleic acid, wherein a different tagging primer is used for eachpolymorphic variant. A different probe oligonucleotide with acorresponding nucleotide tag can be used for each polymorphic variant.This embodiment has the advantage of reducing the number of differentprobe oligonucleotides that would need to be synthesized to identifypolymorphic variance in amplicons produced for a plurality of targetsequences. Alternatively, different sets of tagging and reverse primerscan be employed for each target, wherein each set has a set ofnucleotide tags for each polymorphic variant that is different from theprimers in the other set, and different probe oligonucleotides are usedfor each sample, wherein the probe oligonucleotides have thecorresponding sets of nucleotide tag sequences and different reportermolecules. In either case, the amplification produces a set of Tamplicons from each sample that bear allele-specific reporters.Regulatory oligonucleotides specifically recognizing the differentregulatory sequences in each probe oligonucleotide are provided with acorresponding quencher molecule.

In embodiments, wherein the same set of tagging and reverse primers isused for each sample, the tagging and reverse primers for each targetcan be initially combined separately from the sample, and each probeoligonucleotide/regulatory oligonucleotide set can be initially combinedwith its corresponding sample. Aliquots of the initially combinedtagging and reverse primers can then be added to aliquots of theinitially combined sample and probe oligonucleotide/regulatoryoligonucleotide sets. These amplification mixtures can be formed in anyarticle that can be subjected to conditions suitable for amplification.For example, the amplification mixtures can be formed in, or distributedinto, separate compartments of a microfluidic device prior toamplification. Suitable microfluidic devices include, in illustrativeembodiments, matrix-type microfluidic devices, such as those describedbelow.

Any amplification method can be employed to produce amplicons from theamplification mixtures. In illustrative embodiments, PCR is employed.

PCR thermal cycling protocols are well known in the art. Typically, PCRconsists of a series of 20-40 cycles. For example, and not limitationthe cycle may include a denaturation step, an annealing step (allowingannealing of the primers to the single-stranded DNA template) and anextension/elongation step.

The amplification is generally carried out for at least three cycles tointroduce the nucleotide tag. In various embodiments, amplification iscarried out for 5, 10, 15, 20, 25, 30, 35, 40, 45, or 50 cycles, or forany number of cycles falling within a range having any of these valuesas endpoints (e.g. 5-10 cycles). In particular embodiments,amplification is carried out for a sufficient number of cycles tonormalize target amplicon copy number across targets and across samples(e.g., 15, 20, 25, 30, 35, 40, 45, or 50 cycles, or for any number ofcycles falling within a range having any of these values as endpoints).

An exemplary protocol, for illustration and not limitation, includes ahotstart step [95° C. for 5 min], a 35 cycle touchdown PCR strategy [1cycle of 95° C. for 15 sec, 64° C. for 45 sec, and 72° C. for 15 sec; 1cycle of 95° C. for 15 sec, 63° C. for 45 sec, and 72° C. for 15 sec; 1cycle of 95° C. for 15 sec, 62° C. for 45 sec, and 72° C. for 15 sec; 1cycle of 95° C. for 15 sec, 61° C. for 45 sec, and 72° C. for 15 sec;and 34 cycles of 95° C. for 15 sec, 62° C. for 45 sec, and 72° C. for 15sec], and a cooling step [1 cycle of 25° C. for 10 sec].

Particular embodiments of the above-described method providesubstantially uniform amplification, yielding one or more targetamplicons wherein the majority of amplicons are present at a levelrelatively close to the average copy number calculated for the one ormore target amplicons. Thus, in various embodiments, at least 50, atleast 55, at least 60, at least 65, at least 70, at least 75, at least80, at least 85, at least 90, at least 91, at least 92, at least 93, atleast 94, at least 95, at least 96, at least 97, at least 98, or atleast 99 percent of the target amplicons are present at greater than 50percent of the average number of copies of target amplicons and lessthan 2-fold the average number of copies of target amplicons.

The invention also provides, in certain embodiments, a method foramplifying a plurality of target nucleotides in which the incorporationof the probe oligonucleotide is, optionally, omitted and the targetnucleotide sequences are tagged during the amplification. Morespecifically, the invention provides a method for amplifying a pluralityof target nucleic acids, typically, in a plurality of samples, thatentails preparing an amplification mixture for each target nucleic acid.Each amplification mixture includes a tagging primer including atarget-specific sequence and a reverse primer including atarget-specific sequence. The amplification mixtures are subjected toamplification to produce amplicons of one or more target nucleotides.The target nucleotide sequences are then provided one or more sets ofprobe oligonucleotide/regulatory oligonucleotide, wherein the probeoligonucleotides recognize the nucleotide tag associated with eachpolymorphic variant. In various embodiments, a second amplificationreaction can be performed to incorporate the probe oligonucleotide. Inalternative embodiments, the probe oligonucleotide hybridizes to thetagged target nucleic acid, wherein the regulatory oligonucleotide actsas a competing agent. In such embodiments, it will be especiallyadvantageous for the regulatory oligonucleotide to have an auxiliarysequence that partially overlaps with the nucleotide tag recognitionsequence on the probe oligonucleotide. It will be further advantageousfor the auxiliary sequence to have a reduced complementarity to theprobe oligonucleotide, compared to the tagged target nucleic acid alongthe same nucleotides, when the probe oligonucleotide and the regulatoryoligonucleotide are aligned along the regulatory sequence. In preferredembodiments, this auxiliary sequence will be located at the 5′ end ofthe regulatory oligonucleotide.

The competitiveness of the regulatory oligonucleotide for the probeoligonucleotide can be adjusted varying the strength of the interactionbetween the regulatory oligonucleotide and the probe oligonucleotide, aswell as the interaction between the nucleotide tag and the probeoligonucleotide. The competition can be standardized such that theacquired signal is relatively proportional to the average copy number ofa tagged target nucleic acid with a particular polymorphic variant.

Long-Range PCR

In various embodiments, the target nucleotide sequence amplified can be,e.g., 25 bases, 50 bases, 100 bases, 200 bases, 500 bases, or 750 bases.In certain embodiments of the above-described methods, a long-rangeamplification method, such as long-range PCR can be employed to produceamplicons from the amplification mixtures. Long-range PCR permits theamplification of target nucleotide sequences ranging from one or a fewkilobases (kb) to over 50 kb. In various embodiments, the targetnucleotide sequences that are amplified by long-range PCR are at leastabout 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 25, 30, 35,40, 45, or 50 kb in length. Target nucleotide sequences can also fallwithin any range having any of these values as endpoints (e.g., 25 basesto 100 bases or 5-15 kb). The use of long-range PCR in theabove-described methods can, in some embodiments, yield a plurality oftarget amplicons wherein at least 50, at least 55, at least 60, at least65, or at least 70 percent of the target amplicons are present atgreater than 50 percent of the average number of copies of targetamplicons and less than 2-fold the average number of copies of targetamplicons.

Long-range PCR is well known in the art. See, e.g., Cheng at al. (June1994). “Effective amplification of long targets from cloned inserts andhuman genomic DNA”. Proc. Natl. Acad. Sci. U.S.A. 91: 5695-9. Enzymes,protocols, and kits for long-range PCR that are suitable for use in themethods described here are commercially available; examples include:SequalPrep™ Long PCR Kit (Invitrogen, USA), PfuUltra® II Fusion HS DNApolymerase (Stratagene), Phusion® DNA polymerases, Phusion® Flash HighFidelity PCR Master Mix (Finnzymes).

In certain embodiments, the amount of target amplicons produced in theamplification mixtures can be quantified during amplification, e.g., byquantitative real-time PCR, or after.

Digital PCR

In some embodiments, samples are loaded into an amplification device,for example, a PCR plate or a microfluidic device, at sampleconcentrations containing on average in the range of 0.8 to 1.6amplification templates per well, or in some embodiments oneamplification template per well or chamber. Each well or chamber in thedevice is prepared such that it contains suitable tagging and reverseprimers and a relevant combination of probe oligonucleotide/regulatoryoligonucleotide sets. For discussions of “digital PCR” see, for example,Vogelstein and Kinzler, 1999, Proc Natl Acad Sci USA 96:9236-41; McBrideet al., U.S. Patent Application Publication No. 20050252773, especiallyExample 5 (each of these publications are hereby incorporated byreference in their entirety). Digital amplification methods can make useof certain-high-throughput devices suitable for digital PCR, such asmicrofluidic devices typically including a large number and/or highdensity of small-volume reaction sites (e.g., nano-volume reaction sitesor reaction chambers). In illustrative embodiments, digitalamplification is performed using a microfluidic device, such as theDigital Array microfluidic devices described below. Digitalamplification can entail distributing or partitioning a sample amonghundreds to thousands of reaction mixtures disposed in a reaction/assayplatform or microfluidic device. In counting the number of positiveamplification results, e.g., at the reaction endpoint, one is countingthe individual template molecules present in the input sampleone-by-one. A major advantage of digital amplification is that thequantification is independent of variations in the amplificationefficiency—successful amplifications are counted as one molecule,independent of the actual amount of product.

In certain embodiments, digital amplification can be carried out afterpreamplification of sample nucleic acids. Typically, preamplificationprior to digital amplification is performed for a limited number ofthermal cycles (e.g., 5 cycles, or 10 cycles). In certain embodiments,the number of thermal cycles during preamplification can range fromabout 4 to 15 thermal cycles, or about 4-10 thermal cycles. In certainembodiments the number of thermal cycles can be 3, 4, 5, 6, 7, 8, 9, 10,11, 12, 13, 14, 15, or more than 15. The above-described amplificationto produce adaptor sequence-containing amplicons for DNA sequencing canbe substituted for the typical preamplification step.

Digital amplification methods are described in U.S. Publication No.20090239308, which is hereby incorporated by reference in its entiretyand, in particular, for its disclosure of digital amplification methodsand devices. Generally, in digital amplification, identical (orsubstantially similar) amplification reactions are run on a nucleic acidsample, such as genomic DNA. The number of individual reactions for agiven nucleic acid sample may vary from about 2 to over 1,000,000.Typically, the number of reactions performed on a sample is about 100 orgreater, more typically about 200 or greater, and even more typicallyabout 300 or greater. Larger scale digital amplification can also beperformed in which the number of reactions performed on a sample isabout 500 or greater, about 700 or greater, about 765 or greater, about1,000 or greater, about 2,500 or greater, about 5,000 or greater, about7,500 or greater, or about 10,000 or greater. The number of reactionsperformed may also be significantly higher, such up to about 25,000, upto about 50,000, up to about 75,000, up to about 100,000, up to about250,000, up to about 500,000, up to about 750,000, up to about1,000,000, or even greater than 1,000,000 assays per genomic sample.

In particular embodiments, the quantity of nucleic acid subjected todigital amplification is generally selected such that, when distributedinto discrete reaction mixtures, each individual amplification reactionis expected to include one or fewer amplifiable nucleic acids. One ofskill in the art can determine the concentration of target amplicon(s)produced as described above and calculate an appropriate amount for usein digital amplification. More conveniently, a set of serial dilutionsof the target amplicon(s) can be tested. For example, a device that iscommercially available from Fluidigm Corp. as the 12.765 Digital Arraymicrofluidic device allows 12 different dilutions to be testedsimultaneously. Optionally, a suitable dilution can be determined bygenerating a linear regression plot. For the optimal dilution, the lineshould be straight and pass through the origin. Subsequently theconcentration of the original samples can be calculated from the plot.

The appropriate quantity of target amplicon(s) can be distributed intodiscrete locations or reaction wells or chambers such that each reactionincludes, for example, an average of no more than about one amplicon pervolume. The target amplicon(s) can be combined with (an) probeoligonucleotide/regulatory oligonucleotide set(s), prior to distributionor after.

Following distribution, the reaction mixtures are subjected toamplification to identify those reaction mixtures that contained atarget amplicon. Any amplification method can be employed, butconveniently, PCR is used, e.g., real-time PCR or endpoint PCR. Thisamplification can employ probe oligonucleotides capable of amplifyingthe target amplicon(s). In particular embodiments, all or some of theprobe oligonucleotide, regulatory oligonucleotide, tagging primer andreverse primer are provided. In alternative embodiments, the probeoligonucleotide can anneal to the nucleotide tag introduced in aprevious amplification step.

The concentration of any target amplicon (copies/μl) is correlated withthe number of positive (i.e., amplification product-containing) reactionmixtures. See U.S. patent publication No. 20090239308, which isincorporated by reference for all purposes and, in particular, foranalysis of digital PCR results. Also see Dube et al., 2008,“Mathematical Analysis of Copy Number Variation in a DNA Sample UsingDigital PCR on a Nanofluidic Device” PLoS ONE 3(8): e2876.doi:10.1371/journal.pone.0002876, which is incorporated by reference forall purposes and, in particular, for analysis of digital PCR results.

In an illustrative embodiment of sample calibration for DNA sequencingby digital PCR, a PCR reaction mix containing roughly 100-360 ampliconsper μl can be loaded onto a Digital Array microfluidic device, such asFluidigm Corporation's (South San Francisco, Calif.) 12.765 DigitalArray microfluidic device, described below. The microfluidic chip has 12panels and each panel contains 765 chambers. Replicate panels on thedigital chip can be assayed in order to obtain absolute quantificationof the initial concentration of a target nucleic acid.

Sample Nucleic Acids

Preparations of nucleic acids (“samples”) can be obtained frombiological sources and prepared using conventional methods known in theart. In particular, DNA or RNA useful in the methods described hereincan be extracted and/or amplified from any source, including bacteria,protozoa, fungi, viruses, organelles, as well higher organisms such asplants or animals, particularly mammals, and more particularly humans.Suitable nucleic acids can also be obtained from environmental sources(e.g., pond water, air sample), from man-made products (e.g., food),from forensic samples, and the like. Nucleic acids can be extracted oramplified from cells, bodily fluids (e.g., blood, a blood fraction,urine, etc.), or tissue samples by any of a variety of standardtechniques. Illustrative samples include samples of plasma, serum,spinal fluid, lymph fluid, peritoneal fluid, pleural fluid, oral fluid,and external sections of the skin; samples from the respiratory,intestinal genital, and urinary tracts; samples of tears, saliva, bloodcells, stem cells, or tumors. For example, samples of fetal DNA can beobtained from an embryo or from maternal blood. Samples can be obtainedfrom live or dead organisms or from in vitro cultures. Illustrativesamples can include single cells, paraffin-embedded tissue samples, andneedle biopsies. Nucleic acids useful in the invention can also bederived from one or more nucleic acid libraries, including cDNA, cosmid,YAC, BAC, P1, PAC libraries, and the like.

Nucleic acids of interest can be isolated using methods well known inthe art, with the choice of a specific method depending on the source,the nature of nucleic acid, and similar factors. The sample nucleicacids need not be in pure form, but are typically sufficiently pure toallow the amplification steps of the methods of the invention to beperformed. Where the target nucleic acids are RNA, the RNA can bereversed transcribed into cDNA by standard methods known in the art andas described in Sambrook, J., Fritsch, E. F., and Maniatis, T.,Molecular Cloning: A Laboratory Manual. Cold Spring Harbor LaboratoryPress, NY, Vol. 1, 2, 3 (1989), for example. The cDNA can then beanalyzed according to the methods of the invention.

Target Nucleic Acids

Any target nucleic acid that can be tagged in an encoding reaction ofthe invention (described herein) can be detected using the methods ofthe invention. In typical embodiments, at least some nucleotide sequenceinformation will be known for the target nucleic acids. For example, ifthe encoding reaction employed is PCR, sufficient sequence informationis generally available for each end of a given target nucleic acid topermit design of suitable amplification primers. In an alternativeembodiment, the target-specific sequences in primers could be replacedby random or degenerate nucleotide sequences.

The targets can include, for example, nucleic acids associated withpathogens, such as viruses, bacteria, protozoa, or fungi; RNAs, e.g.,those for which over- or under-expression is indicative of disease,those that are expressed in a tissue- or developmental-specific manner;or those that are induced by particular stimuli; genomic DNA, which canbe analyzed for specific polymorphisms (such as SNPs), alleles, orhaplotypes, e.g., in genotyping. Of particular interest are genomic DNAsthat are altered (e.g., amplified, deleted, and/or mutated) in geneticdiseases or other pathologies; sequences that are associated withdesirable or undesirable traits; and/or sequences that uniquely identifyan individual (e.g., in forensic or paternity determinations).

Primer Design

Primers suitable for nucleic acid amplification are sufficiently long toprime the synthesis of extension products in the presence of the agentfor polymerization. The exact length and composition of the primer willdepend on many factors, including, for example, temperature of theannealing reaction, source and composition of the primer, and where aprobe is employed, the nucleotide tag portion of the tagging primer willbe designed applying the same principles to the annealing of the probeoligonucleotide to the nucleotide tag. The ratio of primer:probeconcentration can also be considered. For example, depending on thecomplexity of the target nucleic acid sequence, an oligonucleotideprimer typically contains in the range of about 15 to about 30nucleotides that recognize the targeted nucleotide sequence, although itmay contain more or fewer nucleotides. The primers should besufficiently complementary to selectively anneal to their respectivestrands and form stable duplexes. One skilled in the art knows how toselect appropriate primer pairs to amplify the target nucleic acid ofinterest.

Primers may be prepared by any suitable method, including, for example,cloning and restriction of appropriate sequences or direct chemicalsynthesis by methods such as the phosphotriester method of Narang et al.(1979) Meth. Enzymol. 68: 90-99; the phosphodiester method of Brown etal. (1979) Meth. Enzymol. 68: 109-151; the diethylphosphoramidite methodof Beaucage et al. (1981) Tetra. Lett., 22: 1859-1862; the solid supportmethod of U.S. Pat. No. 4,458,066 and the like, or can be provided froma commercial source.

Primers may be purified by using a Sephadex column (AmershamBiosciences, Inc., Piscataway, N.J.) or other methods known to thoseskilled in the art. Primer purification may improve the sensitivity ofthe methods of the invention.

Assay Formats

Assays of the invention may be carried out in a variety of formats,including multiwell formats and microfluidic formats such as, but notlimited to, droplet systems (see, e.g., Kiss et al., 2008, Anal Chem 80:8975-81.) and integrated microfluidic devices. In some embodiments thePCR amplification reaction is carried out in a reaction volume greaterthan 500 nL, or greater than 1 uL. For example, in some embodiments thePCR amplification reactions are carried out in a multiwell platecomprising 96-1536 wells. In some embodiments, Ta is about 57° C. Inother embodiments, the PCR amplification reaction is carried out in areaction volume less than 100 nL. In some embodiments the PCRamplification reaction is carried out in a microfluidic device. In someembodiments Ta is about 60° C.

Microfluidic Devices

In certain embodiments, any of the methods of the invention can becarried out using a microfluidic device. In illustrative embodiments,the device is a matrix-type microfluidic device is one that allows thesimultaneous combination of a plurality of substrate solutions withreagent solutions in separate isolated reaction chambers. It will berecognized, that a substrate solution can comprise one or a plurality ofsubstrates and a reagent solution can comprise one or a plurality ofreagents. For example, the microfluidic device can allow thesimultaneous pairwise combination of a plurality of differentamplification primers and samples. In certain embodiments, the device isconfigured to contain a different combination of primers and samples ineach of the different chambers. In various embodiments, the number ofseparate reaction chambers can be greater than 50, usually greater than100, more often greater than 500, even more often greater than 1000, andsometimes greater than 5000, or greater than 10,000.

In particular embodiments, the matrix-type microfluidic device is aDynamic Array (“DA”) microfluidic device, an example of which is shownin FIG. 21 of WO 05/107938A2, and described therein. DA microfluidicdevice is a matrix-type microfluidic device designed to isolatepair-wise combinations of samples and reagents (e.g., amplificationprimers, detection probes, etc.) and suited for carrying out qualitativeand quantitative PCR reactions including real-time quantitative PCRanalysis. In some embodiments, the DA microfluidic device is fabricated,at least in part, from an elastomer. DA microfluidic devices aredescribed in PCT publication WO05/107938A2 (Thermal Reaction Device andMethod For Using The Same) and US Pat. Publication US20050252773A1, bothincorporated herein by reference in their entireties for theirdescriptions of DA microfluidic devices. DA microfluidic devices mayincorporate high-density matrix designs that utilize fluid communicationvias between layers of the microfluidic device to weave control linesand fluid lines through the device and between layers. By virtue offluid lines in multiple layers of an elastomeric block, high densityreaction cell arrangements are possible. Alternatively DA microfluidicdevices may be designed so that all of the reagent and sample channelsare in the same elastomeric layer, with control channels in a differentlayer.

U.S. Patent Publication No. 2008/0223721 and PCT Publication No. WO05/107938A2, both incorporated by reference herein, describeillustrative matrix-type devices that can be used to practice themethods described herein. FIG. 21 of WO 05/107938A2 shows anillustrative matrix design having a first elastomeric layer 2110 (1stlayer) and a second elastomeric layer 2120 (2 d layer) each having fluidchannels formed therein. For example, a reagent fluid channel in thefirst layer 2110 is connected to a reagent fluid channel in the secondlayer 2120 through a via 2130, while the second layer 2120 also hassample channels therein, the sample channels and the reagent channelsterminating in sample and reagent chambers 2180, respectively. Thesample and reagent chambers 2180 are in fluid communication with eachother through an interface channel 2150 that has an interface valve 2140associated therewith to control fluid communication between each of thechambers 2180 of a reaction cell 2160. In use, the interface is firstclosed, then reagent is introduced into the reagent channel from thereagent inlet and sample is introduced into the sample channel throughthe sample inlet; containment valves 2170 are then closed to isolateeach reaction cell 2160 from other reaction cells 2160. Once thereaction cells 2160 are isolated, the interface valve 2140 is opened tocause the sample chamber and the reagent chamber to be in fluidcommunication with each other so that a desired reaction may take place.It will be apparent from this (and the description in WO 05/107938A2)that the DA microfluidic device may be used for reacting M number ofdifferent samples with N number of different reagents.

Although the DA microfluidic devices described above in WO 05/107938 arewell suited for conducting the methods described herein, the inventionis not limited to any particular device or design. Any device thatpartitions a sample and/or allows independent pair-wise combinations ofreagents and sample may be used. U.S. Patent Publication No. 20080108063(which is hereby incorporated by reference it its entirety) includes adiagram illustrating the 48.48 Dynamic Array IFC (Integrated FluidicCircuit), a commercially available device available from Fluidigm Corp.(South San Francisco Calif.).

It will be understood that other configurations are possible andcontemplated such as, for example, 48×96; 96×96; 30×120; etc.

In specific embodiments, the microfluidic device can be a Digital Arraymicrofluidic device, which is adapted to perform digital amplification.Such devices can have integrated channels and valves that partitionmixtures of sample and reagents into nanoliter volume reaction chambers.In some embodiments, the Digital Array microfluidic device isfabricated, at least in part, from an elastomer. Illustrative DigitalArray microfluidic devices are described in pending U.S. Applicationsowned by Fluidigm, Inc., such as U.S. patent publication No.20090239308. One illustrative embodiment has 12 input portscorresponding to 12 separate sample inputs to the device. The device canhave 12 panels, and each of the 12 panels can contain 765 6 nL reactionchambers with a total volume of 4.59 μl it per panel. Microfluidicchannels can connect the various reaction chambers on the panels tofluid sources. Pressure can be applied to an accumulator in order toopen and close valves connecting the reaction chambers to fluid sources.In illustrative embodiments, 12 inlets can be provided for loading ofthe sample reagent mixture. 48 inlets can be used to provide a sourcefor reagents, which are supplied to the biochip when pressure is appliedto accumulator. Additionally, two or more inlets can be provided toprovide hydration to the biochip. Hydration inlets are in fluidcommunication with the device to facilitate the control of humidityassociated with the reaction chambers. As will be understood to one ofskill in the art, some elastomeric materials that can be utilized in thefabrication of the device are gas permeable, allowing evaporated gasesor vapor from the reaction chambers to pass through the elastomericmaterial into the surrounding atmosphere. In a particular embodiment,fluid lines located at peripheral portions of the device provide ashield of hydration liquid, for example, a buffer or master mix, atperipheral portions of the biochip surrounding the panels of reactionchambers, thus reducing or preventing evaporation of liquids present inthe reaction chambers. Thus, humidity at peripheral portions of thedevice can be increased by adding a volatile liquid, for example water,to hydration inlets. In a specific embodiment, a first inlet is in fluidcommunication with the hydration fluid lines surrounding the panels on afirst side of the biochip and the second inlet is in fluid communicationwith the hydration fluid lines surrounding the panels on the other sideof the biochip.

While the Digital Array microfluidic devices are well-suited forcarrying out the digital amplification methods described herein, one ofordinary skill in the art would recognize many variations andalternatives to these devices. The microfluidic device which is the12.765 Dynamic Array commercially available from Fluidigm Corp. (SouthSan Francisco, Calif.), includes 12 panels, each having 765 reactionchambers with a volume of 6 nL per reaction chamber. However, thisgeometry is not required for the digital amplification methods describedherein. The geometry of a given Digital Array microfluidic device willdepend on the particular application. Additional description related todevices suitable for use in the methods described herein is provided inU.S. Patent Application Publication No. 2005/0252773, incorporatedherein by reference for its disclosure of Digital Array microfluidicdevices.

In certain embodiments, the methods described herein can be performedusing a microfluidic device that provides for recovery of reactionproducts. Such devices are described in detail in U.S. patentapplication publication No. US 2010-0273219, which is herebyincorporated by reference in its entirety and specifically for itsdescription of microfluidic devices that permit reaction productrecovery and related methods.

Detection

In particular embodiments, real-time quantification methods are used.For example, “quantitative real-time PCR” methods can be used todetermine the quantity of a target nucleic acid present in a sample bymeasuring the amount of amplification product formed during theamplification process itself. This method of monitoring the formation ofamplification product involves the measurement of PCR productaccumulation at multiple time points.

Devices have been developed that can perform a thermal cycling reactionwith compositions containing a fluorescent indicator, emit a light beamof a specified wavelength, read the intensity of the fluorescent dye,and display the intensity of fluorescence after each cycle. Devicescomprising a thermal cycler, light beam emitter, and a fluorescentsignal detector, have been described, e.g., in U.S. Pat. Nos. 5,928,907;6,015,674; and 6,174,670.

In some embodiments, each of these functions can be performed byseparate devices. For example, if one employs a Q-beta replicasereaction for amplification, the reaction may not take place in a thermalcycler, but could include a light beam emitted at a specific wavelength,detection of the fluorescent signal, and calculation and display of theamount of amplification product.

In particular embodiments, combined thermal cycling and fluorescencedetecting devices can be used for precise quantification of targetnucleic acids. In some embodiments, fluorescent signals can be detectedand displayed during and/or after one or more thermal cycles, thuspermitting monitoring of amplification products as the reactions occurin “real-time.” In certain embodiments, one can use the amount ofamplification product and number of amplification cycles to calculatehow much of the target nucleic acid sequence was in the sample prior toamplification.

According to some embodiments, one can simply monitor the amount ofamplification product after a predetermined number of cycles sufficientto indicate the presence of the target nucleic acid sequence in thesample. One skilled in the art can easily determine, for any givensample type, primer sequence, and reaction condition, how many cyclesare sufficient to determine the presence of a given target nucleic acid.

The detection is typically performed under conditions favorable for theassociation of the reporter and quencher molecules. A suitabletemperature can be chosen to improve the hybridization of the probeoligonucleotide and the regulatory oligonucleotide for signalacquisition. In particular embodiments, the acquisition temperature ischosen such that a significant fraction of the unincorporated probeoligonucleotide is hybridized with the regulatory oligonucleotide. Thissignificant fraction limit can be determined according to rangesspecified elsewhere in this application.

According to certain embodiments, one can employ an internal standard toquantify the amplification product indicated by the fluorescent signal.See, e.g., U.S. Pat. No. 5,736,333.

In various embodiments, employing preamplification, the number ofpreamplification cycles is sufficient to add one or more nucleotide tagsto the target nucleotide sequences, so that the relative copy numbers ofthe tagged target nucleotide sequences is substantially representativeof the relative copy numbers of the target nucleic acids in the sample.For example, preamplification can be carried out for 2-20 cycles tointroduce the sample-specific nucleotide tags. In other embodiments,detection is carried out at the end of exponential amplification, i.e.,during the “plateau” phase, or endpoint PCR is carried out. In thisinstance, preamplification will normalize amplicon copy number acrosstargets and across samples. In various embodiments, preamplificationand/or amplification can be carried out for about: 2, 4, 10, 15, 20, 25,30, 35, or 40 cycles or for a number of cycles falling within any rangebounded by any of these values.

Removal of Undesired Reaction Components

It will be appreciated that reactions involving complex mixtures ofnucleic acids in which a number of reactive steps are employed canresult in a variety of unincorporated reaction components, and thatremoval of such unincorporated reaction components, or reduction oftheir concentration, by any of a variety of clean-up procedures canimprove the efficiency and specificity of subsequently occurringreactions. For example, it may be desirable, in some embodiments, toremove, or reduce the concentration of preamplification primers ortagging primers prior to carrying out the amplification steps describedherein.

In certain embodiments, the concentration of undesired components can bereduced by simple dilution. For example, preamplified samples can bediluted about 2-, 5-, 10-, 50-, 100-, 500-, 1000-fold prior toamplification to improve the specificity of the subsequent amplificationstep.

In some embodiments, undesired components can be removed by a variety ofenzymatic means. Alternatively, or in addition to the above-describedmethods, undesired components can be removed by purification. Forexample, a purification tag can be incorporated into any of theabove-described primers (e.g., into the barcode nucleotide sequence) tofacilitate purification of the tagged target nucleotides.

In particular embodiments, clean-up includes selective immobilization ofthe desired nucleic acids. For example, desired nucleic acids can bepreferentially immobilized on a solid support. In an illustrativeembodiment, an affinity moiety, such as biotin (e.g., photo-biotin), isattached to desired nucleic acid, and the resulting biotin-labelednucleic acids immobilized on a solid support comprising an affinitymoiety-binder such as streptavidin. Immobilized nucleic acids can bequeried with probes, and non-hybridized and/or non-ligated probesremoved by washing (See, e.g., Published P.C.T. Application WO 03/006677and US Patent Publication No. 20030036064 Alternatively, immobilizednucleic acids can be washed to remove other components and then releasedfrom the solid support for further analysis. In particular embodiments,an affinity moiety, such as biotin, can be attached to an amplificationprimer such that amplification produces an affinity moiety-labeled(e.g., biotin-labeled) amplicon. Thus, for example, where a taggingprimer, reverse primer and an probe oligonucleotide are employed, asdescribed above, at least one of said oligonucleotides can include anaffinity moiety.

Data Output and Analysis

In certain embodiments, when the methods of the invention are carriedout on a matrix-type microfluidic device, the data can be output as aheat matrix (also termed “heat map”). In the heat matrix, each square,representing a reaction chamber on the matrix, has been assigned a colorvalue which can be shown in gray scale, but is more typically shown incolor. In gray scale, black squares indicate that no amplificationproduct was detected, whereas white squares indicate the highest levelof amplification produce, with shades of gray indicating levels ofamplification product in between. In a further aspect, a softwareprogram may be used to compile the data generated in the heat matrixinto a more reader-friendly format.

Applications

The methods of the invention are applicable to any technique aimed atdetecting the presence or amount of one or more target nucleic acids ina nucleic acid sample. Thus, for example, these methods are applicableto identifying the presence of particular polymorphisms (such as SNPs),alleles, or haplotypes, or chromosomal abnormalities, such asamplifications, deletions, or aneuploidy. The methods may be employed ingenotyping, which can be carried out in a number of contexts, includingdiagnosis of genetic diseases or disorders, pharmacogenomics(personalized medicine), quality control in agriculture (e.g., for seedsor livestock), the study and management of populations of plants oranimals (e.g., in aquaculture or fisheries management or in thedetermination of population diversity), species or strain determinationor paternity or forensic identifications. The methods of the inventioncan be applied in the identification of sequences indicative ofparticular conditions or organisms in biological or environmentalsamples. For example, the methods can be used in assays to identifypathogens, such as viruses, bacteria, and fungi). The methods can alsobe used in studies aimed at characterizing environments ormicroenvironments, e.g., characterizing the microbial species in thehuman gut.

These methods can also be employed in determinations DNA or RNA copynumber. Determinations of aberrant DNA copy number in genomic DNA isuseful, for example, in the diagnosis and/or prognosis of geneticdefects and diseases, such as cancer. Determination of RNA “copynumber,” i.e., expression level is useful for expression monitoring ofgenes of interest, e.g., in different individuals, tissues, or cellsunder different conditions (e.g., different external stimuli or diseasestates) and/or at different developmental stages.

In addition, the methods can be employed to prepare nucleic acid samplesfor further analysis, such as, e.g., DNA sequencing. Diseases with agenetic component can be tested for carrier status or risk diseaseoccurrence in subjects. One aspect of the invention relates topredicting the carrier status or the risk of disease occurrence in asubject. The list of diseases with a genetic component is growing andcomprises Haemophilia, Galactosemia, Duchenne Muscular Dystrophy,Polycystic Kidney Disease, Neurofibromatosis Type I, HereditarySpherocytosis, Marfan syndrome, Huntington's Disease, Abdominal AorticAneurysm, Age-related Macular Degeneration, Alcohol Dependence, AlopeciaAreata, Ankylosing Spondylitis, Asthma, Atopic Dermatitis, AtrialFibrillation, Atrial Fibrillation: Preliminary Research,Attention-Deficit Hyperactivity Disorder, Back Pain, Basal CellCarcinoma, Behçet's Disease, Bipolar Disorder, Bipolar Disorder:Preliminary Research, Bladder Cancer, Brain Aneurysm, Breast Cancer,Celiac Disease, Chronic Kidney Disease, Chronic Lymphocytic Leukemia,Chronic Obstructive Pulmonary Disease (COPD), Cleft Lip and CleftPalate, Cluster Headaches, Colorectal Cancer, Creutzfeldt-Jakob Disease,Crohn's Disease, Developmental Dyslexia, Endometriosis, EsophagealCancer, Esophageal Squamous Cell Carcinoma (ESCC), Essential Tremor,Exfoliation Glaucoma, Follicular Lymphoma, Gallstones, GeneralizedVitiligo, Gestational Diabetes, Gout, Hashimoto's Thyroiditis, HeartAttack, Hypertension, Hodgkin Lymphoma, Hypertriglyceridemia,Intrahepatic Cholestasis of Pregnancy, Keloid, Kidney Disease, KidneyStones, Larynx Cancer, Lou Gehrig's Disease (ALS), Lung Cancer, Lupus(Systemic Lupus Erythematosus), Male Infertility, Melanoma, MultipleSclerosis, Narcolepsy, Nasopharyngeal Carcinoma, Neural Tube Defects,Neuroblastoma, Nicotine Dependence, Nonalcoholic Fatty Liver Disease,Obesity, Obsessive-Compulsive Disorder, Oral and Throat Cancer,Osteoarthritis, Otosclerosis, Paget's Disease of Bone, Parkinson'sDisease, Parkinson's Disease: Preliminary Research, Peripheral ArterialDisease, Placental Abruption, Polycystic Ovary Syndrome, Preeclampsia,Primary Biliary Cirrhosis, Progressive Supranuclear Palsy, ProstateCancer, Psoriasis, Restless Legs Syndrome, Rheumatoid Arthritis,Schizophrenia, Limited Cutaneous Type Scleroderma, Selective IgADeficiency, Sjögren's Syndrome, Stomach Cancer, Gastric CardiaAdenocarcinoma, Stroke, Tardive Dyskinesia, Thyroid Cancer, Tourette'sSyndrome, Type 1 Diabetes, Type 2 Diabetes, Ulcerative Colitis, UterineFibroids, and Venous Thromboembolism, Alpha-1 Antitrypsin Deficiency,Cancer, Bloom's Syndrome, Canavan Disease, Connexin 26-RelatedSensorineural Hearing Loss, Cystic Fibrosis, Factor XI Deficiency,Familial Dysautonomia, Familial Hypercholesterolemia Type B, FamilialMediterranean Fever, FANCC-related Fanconi Anemia, G6PD Deficiency,Gaucher Disease, Glycogen Storage Disease Type 1a, Hemochromatosis,Limb-girdle Muscular Dystrophy, Maple Syrup Urine Disease Type 1B,Mucolipidosis IV, Niemann-Pick Disease Type A, Phenylketonuria,Rhizomelic Chondrodysplasia Punctata Type 1 (RCDP1), Sickle Cell Anemia& Malaria Resistance, Tay-Sachs Disease, and Torsion Dystonia. Genotypesassociated with genetic traits can also be tested in subjects. Yetanother aspect of the invention relates to predicting the carrier statusor the likelihood of occurrence of a trait in a subject. Genetic traitsthat are correlated with a genotype comprise Adiponectin Levels, AlcoholFlush Reaction, Asparagus Metabolite Detection, Avoidance of Errors,Birth Weight, Bitter Taste Perception, Blood Glucose, IQ Dependence onBreastfeeding, C-reactive Protein Level, Chronic Hepatitis B, EarwaxType, Eye Color, Food Preference, Freckling, HDL Cholesterol Level, HIVProgression, Hair Color, Hair Curl, Hair Thickness, Height, Hypospadias,Lactose Intolerance, Leprosy Susceptibility, Longevity, Susceptibilityto Malaria Complications, Malaria Resistance (Duffy Antigen), MalePattern Baldness, Non-verbal IQ, Obesity, Episodic Memory, Age atMenarche, Early Menopause, Muscle Performance, Diego, Kidd, and KellBlood Groups, Norovirus Resistance, Odor Detection, Pain Sensitivity,Persistent Fetal Hemoglobin, Photic Sneeze Reflex, Prostate-SpecificAntigen, Reading Ability, Refractive Error, Resistance to HIV/AIDS,Response to Diet and Exercise, Sex Hormone Regulation, Smoking Behavior,and Tuberculosis Susceptibility.

Further, an individual's response to treatment by a drug can be linkedto particular genotypes. Another aspect of the invention relates topredicting an individual's response to drug treatment in correlationwith a particular genotype. Drug responses can be predicted for a listof drug treatments comprising Alpha-1 Antitrypsin Deficiency, BreastCancer, Bloom's Syndrome, Canavan Disease, Connexin 26-RelatedSensorineural Hearing Loss, Cystic Fibrosis, Factor XI Deficiency,Familial Dysautonomia, Familial Hypercholesterolemia Type B, FamilialMediterranean Fever, FANCC-related Fanconi Anemia, G6PD Deficiency,Gaucher Disease, Glycogen Storage Disease Type 1a, Hemochromatosis,Limb-girdle Muscular Dystrophy, Maple Syrup Urine Disease Type 1B,Mucolipidosis IV, Niemann-Pick Disease Type A, Phenylketonuria,Rhizomelic Chondrodysplasia Punctata Type 1 (RCDP1), Sickle Cell Anemia& Malaria Resistance, Tay-Sachs Disease, and Torsion Dystonia.

Finally, nucleic acid samples can be tagged as a first step, priorsubsequent analysis, to reduce the risk that mislabeling orcross-contamination of samples will compromise the results. For example,any physician's office, laboratory, or hospital could tag samplesimmediately after collection, and the tags could be confirmed at thetime of analysis. Similarly, samples containing nucleic acids collectedat a crime scene could be tagged as soon as practicable, to ensure thatthe samples could not be mislabeled or tampered with. Detection of thetag upon each transfer of the sample from one party to another could beused to establish chain of custody of the sample.

Kits

Kits according to the invention include one or more reagents useful forpracticing one or more assay methods of the invention. A kit generallyincludes a package with one or more containers holding the reagent(s)(e.g., primers and/or probe(s)), as one or more separate compositionsor, optionally, as admixture where the compatibility of the reagentswill allow. The kit can also include other material(s) that may bedesirable from a user standpoint, such as a buffer(s), a diluent(s), astandard(s), and/or any other material useful in sample processing,washing, or conducting any other step of the assay.

Kits according to the invention generally include instructions forcarrying out one or more of the methods of the invention. Instructionsincluded in kits of the invention can be affixed to packaging materialor can be included as a package insert or provided as electronic media.As used herein, the term “instructions” can include the address of aninternet site that provides the instructions.

EXAMPLES Example 1

FIG. 1 illustrates use of the method in a genotyping assay, to detectthe presence of specific allele(s) in a sample. In the cartoon, twotarget nucleic acid sequences (T and T′) are present in the sample, Tbeing characterized by an A allele at a particular SNP and T′ beingcharacterized by a G allele. T and T′ are tagged in a PCR reaction usinga pair of tagging primers, one comprising a nucleotide tag sequence Xand a target nucleotide recognition sequence that hybridizes to, andacts as a primer for, the A allele, and the other comprising anucleotide tag sequence Y and a target nucleotide recognition sequencethat hybridizes to, and acts as a primer for, the G allele. The encodingor tagging PCR reaction (shown as an encoding PCR reaction)“incorporates” the x tag into amplicons (if any) of the A allele, and“incorporates” the y tag into amplicons (if any) of the G allele. Theencoding amplification may make use of a single reverse primer.

As shown in the figure, the reaction contains two probeoligonucleotide-regulatory nucleotides pairs. In the first, the probeoligonucleotide comprises a reporter (R_(G)), a regulatory sequence (Z),and a primer sequence that hybridizes to the tag sequence incorporatedinto the A allele amplicons and acts as primer for the PCR amplificationreaction, while the regulatory oligonucleotide comprises a quencher (Q),a sequence segment (Z) complementary to regulatory sequence, and a tailsegment (L) that is not complementary to the probe. In the second, theprobe oligonucleotide comprises a reporter (R_(R)), a regulatorysequence (W), and a primer sequence that hybridizes to the tag sequenceincorporated into the G allele amplicons and acts as primer for the PCRamplification reaction, while the regulatory oligonucleotide comprises aquencher (Q), which may be the same or different from the quencher ofthe first pair, a sequence segment (W) complementary to regulatorysequence, and a tail segment (L) that is not complementary to the probe.The tail (L) sequences of the two regulatory oligonucleotides may be thesame or different. The probe oligonucleotide and regulatoryoligonucleotide of each pair comprise a reporter-quencher pair so thatthe reporter emits a detectable (e.g., fluorescent) signal when theprobe oligonucleotide is hybridized to the regulatory oligonucleotide,but does not emit the signal when the probe and regulatoryoligonucleotides are hybridized to each other, the reporter is quenched.

As is shown in the figure, probe oligonucleotide-primed PCRamplification of the tagged target nucleic acid sequences results inamplicons in which the reporter(s) is incorporated, thereby separatingthe reporter(s) from the quencher molecule(s). The resulting reportersignal(s) may be detected and are indicative of the presence of thecorresponding allele in the sample. The elements on the figure are notdrawn to scale. In addition, the association of the displaced regulatoryoligonucleotides with the unbound probe sequences is not shown in thisfigure. (See FIG. 2.)

Example 2

Tagging primers are designed for each polymorphic variant for variouspolymorphic sites. In addition to the target-specific sequences, thetagging primers are designed to contain a nucleotide tag sequences atthe 5′ end. When testing a polymorphic site, the tagging primers for thefirst alleles contained a different nucleotide tag sequence than thetagging primers for the second allele. The sequences of the primerscontaining both nucleotide tag sequences and the target-specificsequences are listed in Table 1.

Reverse primers are designed to flank the target polynucleotide and arelisted in Table 2.

Probe oligonucleotide—regulatory oligonucleotide pairs are designed. Theprobe oligonucleotides contain a variety of nucleotide tag sequences atthe 3′ end corresponding to the nucleotide tag sequences on the taggingprimers. The probe oligonucleotides contain regulatory sequences at the3′ end that are recognized by the corresponding regulatoryoligonucleotide. The probe oligonucleotides are labeled with afluorescent reporter molecule at the 3′ end. The fluorescent dyes areselected from FAM, CalOrange, and HEX. The regulatory oligonucleotidesare labeled with a corresponding quencher at the 5′ end.

When testing a polymorphic site, two sets of probeoligonucleotide/regulatory oligonucleotide pairs may be used. Each setcontain a different reporter quencher pair and a different nucleotidetag sequence corresponding to the nucleotide tag sequences in thetagging primers.

The sequences of the probe oligonucleotide/regulatory oligonucleotidepairs are listed in Tables 3 and 4. The oligonucleotides are synthesizedby Operon at 10 nmol scale, and provided resuspended in TE buffer(Teknova) at a concentration of 100 uM.

Human genomic DNA samples may be resuspended at 60 ng/μl in low-EDTA TEbuffer (Teknova), and prepared for PCR according to known methods and asdescribed herein above.

Running the 48.48 Dynamic Array™ IFC

The containment and interface accumulator reservoirs are filled with 300μl of Control Line Fluid (Fluidigm PN 89000020). 5 μl of each Sample Mixis loaded into the sample inlets, and 4 μA of the appropriate 10× AssayMix is loaded into each assay inlets on the 48.48 Dynamic Array™ IFC(Fluidigm, PN BMK-M-48.48).

The IFC is thermal cycled and imaged using an FC1™ Cycler manufacturedby Fluidigm Corporation. The IFC thermal cycling protocol includes ahotstart step [95° C. for 5 min], a 35 cycle touchdown PCR strategy [1cycle of 95° C. for 15 sec, 64° C. for 45 sec, and 72° C. for 15 sec; 1cycle of 95° C. for 15 sec, 63° C. for 45 sec, and 72° C. for 15 sec; 1cycle of 95° C. for 15 sec, 62° C. for 45 sec, and 72° C. for 15 sec; 1cycle of 95° C. for 15 sec, 61° C. for 45 sec, and 72° C. for 15 sec;and 34 cycles of 95° C. for 15 sec, 62° C. for 45 sec, and 72° C. for 15sec], and a cooling step [1 cycle of 25° C. for 10 sec]. The data iscollected in an EP1™ Reader manufactured by Fluidigm Corporation andanalyzed using the SNP Genotyping Analysis Software v.3.1.0.

TABLE 1  Tagging Primers SEQ ID Tagging Primer Name Reverse Primer NameTagging Primer Sequence NO FASP_A_SNP3_ALA FASP_SNP3_C2TGCGACTAAGAACGCTATCAGCCTAGGCATTGATTTTGAAGACATCAA 1 FASP_A_SNP3_ALGFASP_SNP3_C2 CAAGTGATCCGAGAGGTTGAACTAGGCATTGATTTTGAAGACATCAG 2FASP_A_SNP6_ALC FASP_SNP6_C1TGCGACTAAGAACGCTATCAGGCCATCATTTAGCTTTACACACTGG 3 FASP_A_SNP6_ALGFASP_SNP6_C1 CAAGTGATCCGAGAGGTTGAAGCCATCATTTAGCTTTACACACTGC 4FASP_A_SNP8_ALA FASP_SNP8_C1 TGCGACTAAGAACGCTATCAGTTCCACAGTGTATGGCCTGTCA5 FASP_A_SNP8_ALG FASP_SNP8_C1 CAAGTGATCCGAGAGGTTGAACCACAGTGTATGGCCTGTCG6 FASP_B_SNP3_ALA FASP_SNP3_C2GGTCACTGTCACGAGGGATATCCTAGGCATTGATTTTGAAGACATCAA 7 FASP_B_SNP6_ALCFASP_SNP6_C1 GGTCACTGTCACGAGGGATATGCCATCATTTAGCTTTACACACTGG 8FASP_B_SNP8_ALA FASP_SNP8_C1 GGTCACTGTCACGAGGGATATTTCCACAGTGTATGGCCTGTCA9 FASP_B_SNP3_ALG FASP_SNP3_C2GCTCCAACCTCTGACCTACTAACTAGGCATTGATTTTGAAGACATCAG 10 FASP_B_SNP6_ALGFASP_SNP6_Cl GCTCCAACCTCTGACCTACTAAGCCATCATTTAGCTTTACACACTGC 11FASP_B_SNP8_ALG FASP_SNP8_C1 GCTCCAACCTCTGACCTACTAACCACAGTGTATGGCCTGTCG12 FASP_3_SNP4_ALA FASP_SNP4_C1GGTCACTGTCACGAGGGATATTTTCAAGTTCCTGACCTTCACATACT 13 FASP_4_SNP4_ALGFASP_SNP4_C1 GCTCCAACCTCTGACCTACTAACAAGTTCCTGACCTTCACATACC 14FASP_3_SNP5_ALC FASP_SNP5_C2GGTCACTGTCACGAGGGATATCACAGAAAGACATATTGGAAGTAACTTAC 15 FASP_4_SNP5_ALTFASP_SNP5_C2 GCTCCAACCTCTGACCTACTAACACAGAAAGACATATTGGAAGTAACTTAT 16FASP_3_SNP6_ALC FASP_SNP6_C1GGTCACTGTCACGAGGGATATGCCATCATTTAGCTTTACACACTGG 8 FASP_4_SNP6_ALGFASP_SNP6_C1 GCTCCAACCTCTGACCTACTAAGCCATCATTTAGCTTTACACACTGC 11FASP_31_AY841151_ALG FASP_31_AY841151_CGGTCACTGTCACGAGGGATATCACAGTTGATTAATGATAGCAGAAC 17 FASP_31_AY841151_ALTFASP_31_AY841151_C GCTCCAACCTCTGACCTACTAACCTCACAGTTGATTAATGATAGCAGAAA 18FASP_35_DQ422949_ALA FASP_35_DQ422949_C GGTCACTGTCACGAGGGATATCATAAACAAATGCCTTGTGGGGATCT 19 FASP_35_DQ422949_ALGFASP_35_DQ422949_C GCTCCAACCTCTGACCTACTAAATAAACAAATGCCTTGTGGGGATCC 20FASP_55_DQ489377_ALC FASP_55_DQ489377_C GGTCACTGTCACGAGGGATATATTGAACCTTTAGTTGTGGTTTGTC 21 FASP_55_DQ489377_ALTFASP_55_DQ489377_C GCTCCAACCTCTGACCTACTAAGAACCTTTAGTTGTGGTTTGTT 22FASP_9_DQ404150_ALC FASP_9_DQ404150_CGCTCCAACCTCTGACCTACTAAAGGCATAGGAGACAATTAGGAAGC 23 FASP_9_DQ404150_ALAFASP_9_DQ404150_C GGTCACTGTCACGAGGGATATCAAAGGCATAGGAGACAATTAGGAAGA 24FASP_19_AY863214_ALG FASP_19_AY863214_CGCTCCAACCTCTGACCTACTAACCTTCCTCTCTTGGGACCG 25 FASP_19_AY863214_ALAFASP_19_AY863214_C GGTCACTGTCACGAGGGATATCCTTCCTCTCTTGGGACCA 26FASP_55_DQ489377_ALT FASP_55_DQ489377_CGCTCCAACCTCTGACCTACTAAGAACCTTTAGTTGTGGTTTGTT 22 FASP_55_DQ489377_ALCFASP_55_DQ489377_C GGTCACTGTCACGAGGGATATATTGAACCTTTAGTTGTGGTTTGTC 21FASP_31_AY841151_ALG FASP_31_AY841151_CGGTCACTGTCACGAGGGATATCACAGTTGATTAATGATAGCAGAAC 17 FASP_31_AY841151_ALTFASP_31_AY841151_C GCTCCAACCTCTGACCTACTAACCTCACAGTTGATTAATGATAGCAGAAA 18FASP_35_DQ422949_ALA FASP_35_DQ422949_CGGTCACTGTCACGAGGGATATCATAAACAAATGCCTTGTGGGGATCT 19 FASP_35_DQ422949_ALGFASP_35_DQ422949_C GCTCCAACCTCTGACCTACTAAATAAACAAATGCCTTGTGGGGATCC 20FASP_1_DQ381153_ALA FASP_1_DQ381153_CGGTCACTGTCACGAGGGATATGGACCTGGCCAGGCATTAA 27 FASP_1_DQ381153_ALCFASP_1_DQ381153_C GCTCCAACCTCTGACCTACTAAGACCTGGCCAGGCATTAC 28FASP_65_AY853302_ALA FASP_65_AY853302_CGGTCACTGTCACGAGGGATATGCAAATAATTTATAGAGAACCTAGTGTGAAT 29FASP_65_AY853302_ALG FASP_65_AY853302_CGCTCCAACCTCTGACCTACTAACAAATAATTTATAGAGAACCTAGTGTGAAC 30FASP_72_AY929334_ALC FASP 72 AY929334_CGGTCACTGTCACGAGGGATATCCTGGGAAAGAAAAGGGTTGAG 31 FASP_72_AY929334_ALTFASP 72 AY929334_C GCTCCAACCTCTGACCTACTAACTCCTGGGAAAGAAAAGGGTTGAA 32FASP_AA_52_DQ435443_ALA FASP_AA_52_DQ435443_CTGCGACTAAGAACGCTATCAGGTAGCAGAAGGCGAAATAATTCATAATTA 33FASP_AA_52_DQ435443_ALC FASP_AA_52_DQ435443_CCAAGTGATCCGAGAGGTTGAAGTAGCAGAAGGCGAAATAATTCATAATTC 34FASP_AA_61_AY842475_ALA FASP_AA_61_AY842475_CTGCGACTAAGAACGCTATCAGCATCTCTAAGCTGTATGTGTGAGCA 35FASP_AA_61_AY842475_ALG FASP_AA_61_AY842475_CCAAGTGATCCGAGAGGTTGAAATCTCTAAGCTGTATGTGTGAGCG 36

TABLE 2  Reverse Primers Reverse Primer Name Tagging Primer NamesReverse Primer Sequence SEQ ID NO. FASP_SNP3_C2 FASP_A_SNP3_ALAGTCTCTGAAGTCAACCTCACCAGAA 37 FASP_A_SNP3_ALG FASP_B_SNP3_ALAFASP_B_SNP3_ALG FASP_SNP6_C1 FASP_A_SNP6_ALC GCTAGTCAGACAAGTGACAGGGAAT38 FASP_A_SNP6_ALG FASP_B_SNP6_ALC FASP_B_SNP6_ALG FASP_3_SNP6_ALCFASP_4_SNP6_ALG FASP_SNP8_C1 FASP_A_SNP8_ALA TTGTGCACCCACACTGGGAGCT 39FASP_A_SNP8_ALG FASP_B_SNP8_ALA FASP_B_SNP8_ALG FASP_SNP4_C1FASP_3_SNP4_ALA GTATAGCTTGCCAAAAGTAGGTACTTCAA 40 FASP_4_SNP4_ALGFASP_SNP5_C2 FASP_3_SNP5_ALC GCACTCAGAAAACTCACTGAAAGGTTATT 41FASP_4_SNP5_ALT FASP_31_AY841151_C FASP_31_AY841151_ALGTTGCCTTCCAAAGATGGTTCATGGAATT 42 FASP_31_AY841151_ALT FASP_35_DQ422949_CFASP 35 DQ422949_ALA CCTGAAGGAATATCCACCCTGCAAA 43 FASP_35_DQ422949_ALGFASP_55_DQ489377_C FASP_55_DQ489377_ALC AGAAGGAAAAGTGGCAGAGTTTGGAAAT 44FASP_55_DQ489377_ALT FASP_9_DQ404150_C FASP_9_DQ404150_ALCACTGCTTAAAGTTCTAAACCAATCAACAAT 45 FASP_9_DQ404150_ALA FASP_19_AY863214_CFASP_19_AY863214_ALG AGGATGAAGTGGCAGGGGAC 46 FASP_19_AY863214_ALAFASP_55_DQ489377_C FASP 55 DQ489377_ALT AGAAGGAAAAGTGGCAGAGTTTGGAAAT 44FASP_55_DQ489377_ALC FASP_31_AY841151_C FASP 31 AY841151_ALGTTGCCTTCCAAAGATGGTTCATGGAATT 42 FASP_31_AY841151_ALT FASP_35_DQ422949_CFASP_35_DQ422949_ALA CCTGAAGGAATATCCACCCTGCAAA 43 FASP_35_DQ422949_ALGFASP_1_DQ381153_C FASP_1_DQ381153_ALA CAAGCTCCCAAGGGCATCTC 47FASP_1_DQ381153_ALC FASP_65_AY853302_C FASP_65_AY853302_ALAGCTTCCTGTATTCCCTTTGTTGTCTAAT 48 FASP_65_AY853302_ALG FASP_72_AY929334_CFASP_72_AY929334_ALC GCCCCACTCTCAAAATCTGAGACTT 49 FASP_72_AY929334_ALTFASP_AA_52_DQ435443_C FASP_AA_52_DQ435443_ALA CTATCTAGTGGTCACCAACCTAGCTA50 FASP_AA_52_DQ435443_ALC FASP_AA_61_AY842475_C FASP_AA_61_AY842475_ALAGATACATCCTCTTACCTAATCTGAGCTTT 51 FASP_AA_61_AY842475_ALG

TABLE 3  Probe oligonucleotides (“Probe oligonucleotides”) RegulatoryTagging Primer SEQ Probe oligonucleotide oligonucleotide Names WithProbe oligonucleotide ID Oligonucleotide Name Names Recognized TagsSequence NO. FASP_A_F2_FAM FASP_A_Q2 FASP_A_SNP3_ALACCAGAATCATCGTGGATGCGA 52 FASP_A_Q2.2 FASP_A_SNP6_ALC CTAAGAACGCTATCAGFASP_A_Q1 FASP_A_SNP8_ALA FASP_AA_19_AY863214_ALAFASP_AA_52_DQ435443_ALA FASP_AA_61_AY842475_ALA FASP_A_F1_CalOrangeFASP_A_Q1 FASP_A_SNP3_ALG TAGGTCGAGGGATCTTCAAGT 53 FASP_A_SNP6_ALGGATCCGAGAGGTTGAA FASP_A_SNP8_ALG FASP_B_F3_FAM FASP_B_Q3 FASP_B_SNP3_ALAGTAGCACAACTCGCAGGTCAC 54 FASP_B_Q3.1 FASP_B_SNP6_ALC TGTCACGAGGGATATFASP_B_Q3.2 FASP_B_SNP8_ALA FASP_B_Q3.3 FASP_3_SNP4_ALA FASP_B_Q3.2_FASP_3_SNP5_ALC TIDE2 FASP_1_DQ381153_ALA FASP_65_AY853302_ALAFASP_72_AY929334_ALC FASP_B_F4_CalOrange FASP_B_Q3 FASP_B_SNP3_ALGGTATGGTTTCCCGCTGCTCC 55 FASP_B_Q4.1 FASP_B_SNP6_ALG AACCTCTGACCTACTAAFASP_B_Q4.2 FASP_B_SNP8_ALG FASP_B_Q4.3 FASP_4_SNP4_ALG FASP_4_SNP5_ALTFASP_4_SNP6_ALG FASP_31_AY841151_ALT FASP_35_DQ422949_ALGFASP_55_DQ489377_ALT FASP_B_F3_FAM_A FASP_B_Q3.2_A FASP_31_AY841151_ALGATAGCACAACTCGCAGGTCA 56 FASP_B_Q5 FASP_35_DQ422949_ALA CTGTCACGAGGGATATFASP_55_DQ489377_ALC FASP_B_F3_FAM_swap FASP_B_Q3.2 FASP_9_DQ404150_ALCGTAGCACAACTCGCAGCTCC 57 FASP_19_AY863214_ALG AACCTCTGACCTACTAAFASP_55_DQ489377_ALT FASP_B_F4_CalOrange_ FASP_B_Q4.2FASP_9_DQ404150_ALA GTATGGTTTCCCGCTGGTCA 58 swap FASP_19_AY863214_ALACTGTCACGAGGGATAT FASP_55_DQ489377_ALC FASP_B_F4_HEX FASP_B_Q4.2_FASP_1_DQ381153_ALC GTATGGTTTCCCGCTGCTCC 55 TIDE3 FASP_65_AY853302_ALGAACCTCTGACCTACTAA FASP_72_AY929334_ALT FASP_A_F1_HEX FASP_A_Q1.2FASP_AA_19_AY863214_ALG TAGGTCGAGGGATCTTCAAG 53 FASP_AA_52_DQ435443_ALCTGATCCGAGAGGTTGAA FASP_AA_61_AY842475_ALG

TABLE 4  Regulatory Oligonucleotides Regulatory SEQ oligonucleotide Probe Regulatory ID Name Oligonucleotide Names Oligonucleotide SequenceNO. FASP_A_Q2 FASP_A_F2_FAM ACGCGGTCCACGATGATTCTGG 59 FASP_A_Q1FASP_A_F1_CalOrange ACGCCCAAGATCCCTCGACCTA 60 FASP_B_Q3 FASP_B_F3_FAMCACCGGTGCGAGTTGTGCTAC 61 FASP_B_Q4 FASP_B_F4_CalOrangeGTCCCGAGCGGGAAACCATAC 62 FASP_B_Q3.1 FASP_B_F3_FAMACGCCGGACCTGCGAGTTGTGCTAC 63 FASP_B_Q4.1 FASP_B_F4_CalOrangeGCACCCGAGCAGCGGGAAACCATAC 65 FASP_B_Q3.2 FASP_B_F3_FAMCGGCAGCCGGTGCGAGTTGTGCTAC 65 FASP_B_F3_FAM_swap FASP_B_Q4.2FASP_B_F4_CalOrange GCTCCCCCCGAGCGGGAAACCATAC 66FASP_B_F4_CalOrange_swap FASP_B_Q3.3 FASP_B_F3_FAMACCCCGGCTGCGGGTTGTGCTGCC 67 FASP_B Q4.3 FASP_B_F4_CalOrangeACGCCCCCGGCGGGAAACCGTGC 68 FASP_B_Q3.2_A FASP_B_F3_FAM_ACGGCAGCCGGTGCGAGTTGTGCTAT 69 FASP_BQ5 FASP_B_F3_FAM_ACCTCGGTGCGAGTTGTGCTATGGGG 70 FASP_BQ3.2_TIDE2 FASP_B_F3_FAMACGCCGCCGGTGCGAGTTGTGCTAC 65 FASP_BQ4.2_TIDE3 FASP_B_F4_HEXGCACCCCCCGAGCGGGAAACCATAC 66 FASP_A_Q2.2 FASP_A_F2_FAMGAGCCGGCGGTCCACGATGATTCTGG 71 FASP_A_Q1.2 FASP_A_F1_HEXCTGCGCGCCCAAGATCCCTCGACCTA 72

TABLE 5 Sample Pre-Mix Component Volume per Inlet (uL) Biotium 2X FastProbe Master Mix 3.0 20X SNPtype SampleLoading Reagent 0.3 Probe Mix 0.150X ROX 0.036 PCR-certified water 0.064 Total 3.5

TABLE 6 Assay Mix Component Volume (uL) Tagging Primers (100 uM each)3.0 Reverse Primer 8.0 DNA Suspension Buffer 29.0 Total 40.0

TABLE 7 10X Assays Component Volume per Inlet (uL) 2X Assay LoadingReagent 2.5 PCR-certified water 1.5 Assay Mix 1.0 Total 5.0

It is understood that the invention is not limited to the particularmethodology, protocols, and reagents, etc., described herein, as thesecan be varied by the skilled artisan. It is also understood that theterminology used herein is used for the purpose of describing particularillustrative embodiments only, and is not intended to limit the scope ofthe invention. The embodiments of the invention and the various featuresand advantageous details thereof are explained more fully with referenceto the non-limiting embodiments and examples that are described and/orillustrated in the accompanying drawings and detailed in the followingdescription. It should be noted that the features illustrated in thedrawings are not necessarily drawn to scale, and features of oneembodiment may be employed with other embodiments as the skilled artisanwould recognize, even if not explicitly stated herein. Descriptions ofwell-known components and processing techniques may be omitted so as tonot unnecessarily obscure the embodiments of the invention.

It is understood that the examples and embodiments described herein arefor illustrative purposes only and that various modifications or changesin light thereof will be suggested to persons skilled in the art and areto be included within the spirit and purview of this application andscope of the appended claims.

In addition, all other publications, patents, and patent applicationscited herein are hereby incorporated by reference in their entirety forall purposes.

We claim:
 1. A method for detecting a target nucleotide sequencecomprising: a) tagging the target nucleotide sequence with a nucleotidetag sequence, thereby producing a tagged target nucleic acid sequence;b) providing a probe oligonucleotide comprising a nucleotide tagrecognition sequence complementary to the nucleotide tag sequence and aregulatory sequence 5′ to the nucleotide tag recognition sequence,wherein said probe oligonucleotide comprises a first label and has amelting temperature Tm1; c) amplifying the tagged target nucleic acidsequence in a PCR amplification reaction using the probe oligonucleotideas a primer, wherein said PCR amplification reaction is characterized byan annealing temperature Ta; wherein the PCR amplification reaction iscarried out in the presence of a regulatory oligonucleotide comprising asequence segment that is complementary to the regulatory sequence and atail segment with a sequence not complementary to the probeoligonucleotide sequence, wherein said regulatory oligonucleotidecomprises a second label and has a melting temperature Tm2; and d)detecting the product of the PCR amplification reaction; wherein thefirst label and the second label constitute a fluorescentreporter/quencher pair; and wherein Tm1 and Tm2 are both higher than Ta.2. The method of claim 1, wherein the nucleotide tag sequence isincorporated into the tagged target nucleic acid sequence using a PCRreaction.
 3. The method of claim 1, wherein the nucleotide tagrecognition sequence is exactly complementary to the nucleotide tagsequence.
 4. The method of claim 1, wherein the regulatoryoligonucleotide comprises a sequence segment that is exactlycomplementary to the regulatory sequence.
 5. The method of claim 1,wherein the regulatory oligonucleotide has a length in the range of15-45 nucleotides.
 6. The method of claim 1, wherein the Ta is in therange of 55-64° C.
 7. The method of claim 1, wherein the PCRamplification reaction comprises at least 20 cycles at the Ta.
 8. Themethod of claim 1, wherein the tail segment of the regulatoryoligonucleotide has a length of from 5 to about 25 bases.
 9. The methodof claim 8, wherein the tail segment has a length of 5-8 bases.
 10. Themethod of claim 8, wherein the tail segment is at least about 70% GC.11. The method of claim 1, wherein the tail segment of the regulatoryoligonucleotide is 100% noncomplementary to the region of the probeoligonucleotide to which it corresponds when the regulatoryoligonucleotide is aligned to the probe oligonucleotide.